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Tønnesen EMT, Stougaard M, Meldgaard P, Lade-Keller J. Prognostic value of KRAS mutations, TP53 mutations and PD-L1 expression among lung adenocarcinomas treated with immunotherapy. J Clin Pathol 2023; 77:54-60. [PMID: 36410939 DOI: 10.1136/jcp-2022-208574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2022]
Abstract
AIMS The aim of this study was to investigate the association between oncogenic alterations and programmed cell death ligand 1 (PD-L1) expression in lung adenocarcinomas, as well as the prognostic value of KRAS and/or TP53 mutations in patients treated with immunotherapy. METHODS This study is a retrospective cohort study of 519 patients with lung adenocarcinomas analysed for mutations and PD-L1 expression. Data were collected from electronic pathology record system, next-generation sequencing system, and clinical databases. Association between mutations and PD-L1 expression was investigated, as well as survival statistics of the 65 patients treated with immunotherapy. RESULTS 41% of the samples contained a KRAS mutation, predominantly together with mutations in TP53 (41%) or STK11 (10%). Higher expression of PD-L1 was seen among patients with KRAS mutations (p=0.002) and EGFR wild type (p=0.006). For patients treated with immunotherapy, there was no statistically significant difference for overall survival (OS) and progression-free survival (PFS) according to KRAS mutation status, TP53 mutation status or PD-L1 expression. The HR for concomitant mutations in TP53 and KRAS was 0.78 (95% CI 0.62 to 0.99) for OS and 0.43 (0.21 to 0.88) for PFS. Furthermore, concomitant TP53 and KRAS mutations predicted a better PFS (p=0.015) and OS (p=0.029) compared with no mutations or a single mutation in either TP53 or KRAS. CONCLUSION Mutations in TP53 together with KRAS may serve as a potential biomarker for survival benefits with immunotherapy.
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Affiliation(s)
- Ea Maria Tønning Tønnesen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Pathology, Viborg Regional Hospital, Viborg, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Peter Meldgaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Johanne Lade-Keller
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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2
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Lilja-Fischer JK, Kristensen MH, Lassen P, Steiniche T, Tramm T, Stougaard M, Maare C, Johansen J, Primdahl H, Kristensen CA, Andersen M, Eriksen JG, Overgaard J. HPV testing versus p16 immunohistochemistry in oropharyngeal squamous cell carcinoma: results from the DAHANCA 19 study. Acta Oncol 2023; 62:1384-1388. [PMID: 37837201 DOI: 10.1080/0284186x.2023.2266127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
INTRODUCTION The prognosis after primary (chemo-)radiotherapy for oropharyngeal squamous cell carcinoma (OPSCC) is affected by Human Papillomavirus (HPV) status, with a better prognosis in HPV-positive OPSCC. HPV-status is routinely assessed by p16 immunohistochemistry (IHC), but additional HPV DNA testing is debated. Also, there are numerous HPV genotypes, which prognostic role may need clarification. The purpose of this study was: (1) to test a custom-made targeted HPV next generation sequencing (NGS) panel in OPSCC, (2) to determine correlation with p16 IHC, and (3) to assess the impact of HPV DNA testing on outcome in the prospectively randomized clinical trial DAHANCA 19. MATERIALS AND METHODS We included 271 patients with OPSCC treated with primary (chemo-)radiotherapy in the DAHANCA 19 trial. Of these, 199 (73%) were p16-positive. HPV-status was determined by targeted HPV next generation sequencing (NGS), using a custom-made HPV genotyping panel. RESULTS HPV was detected in 194 tumor samples. p16 IHC and NGS HPV status were concordant in 265 (98%) of 271 patients, whereas we did not detect HPV DNA in 5 p16-positive tumors. HPV16 accounted for 169 of 194 HPV-positive cases (87%). HPV genotypes 18, 31, 33, 35, and 59 were also detected.Loco-regional failure and overall survival were similar whether patients were separated by p16 IHC, or HPV DNA status (p < 0.0001 for all) and did not depend on HPV genotype (p = 0.9 and p = 0.7). CONCLUSION In the present study, HPV DNA testing or typing in a Danish OPSCC cohort did not add additional information to p16 IHC, the most widely used and accepted prognostic indicator.
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Affiliation(s)
- Jacob Kinggaard Lilja-Fischer
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
- Department of Otolaryngology - Head & Neck surgery, Aarhus University Hospital, Aarhus, Denmark
| | | | - Pernille Lassen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Steiniche
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Trine Tramm
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Jørgen Johansen
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Hanne Primdahl
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Maria Andersen
- Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| | - Jesper Grau Eriksen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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3
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Bønløkke S, Steiniche T, Sorensen BS, Nyvang GB, Lindegaard JC, Blaakaer J, Bertelsen J, Fuglsang K, Strube ML, Lenz S, Stougaard M. Circulating cell-free HPV DNA is a strong marker for disease severity in cervical cancer. Mol Oncol 2023. [PMID: 37853962 DOI: 10.1002/1878-0261.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023] Open
Abstract
For cervical cancer (CC), circulating cell-free HPV DNA (ccfHPV) may establish disease severity. Furthermore, HPV integration has been correlated to viral load and survival. In this study, pre-treatment plasma from 139 CC cases (50 primary surgery patients, 22 primary surgery + adjuvant oncological therapy patients, and 67 primary oncological therapy patients) was collected (2018-2020). Furthermore, plasma from 25 cervical intraepithelial neoplasia grade 3 patients and 15 healthy women (negative controls) were collected. Two next-generation sequencing (NGS) panels were used to establish ccfHPV presence and human papillomavirus type 16 (HPV16) integration status. ccfHPV was detected in four primary surgery (8.0%), eight primary surgery + adjuvant oncology (36.4%), and 54 primary oncology (80.6%) patients. For primary oncology patients with HPV16-related cancer (n = 37), more ccfHPVneg than ccfHPVpos patients had HPV16 integration (P = 0.04), and in patients with HPV16 integration (n = 13), ccfHPVpos patients had higher disease stages than ccfHPVneg patients (P = 0.05). In summary, ccfHPV presence is related to disease severity and may add to the debated Sedlis criteria used for identifying patients for adjuvant oncological therapy. However, ccfHPV detection is influenced by HPV integration status and disease stage, and these factors need to be considered in ccfHPVneg patients.
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Affiliation(s)
- Sara Bønløkke
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Torben Steiniche
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | | | - Jan Blaakaer
- Department of Obstetrics and Gynecology, Odense University Hospital, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense M, Denmark
| | | | - Katrine Fuglsang
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Denmark
| | - Mikael Lenz Strube
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Suzan Lenz
- Private Gynecological Clinic "Suzan Lenz Gynaekolog", Copenhagen, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
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4
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Neldeborg S, Soerensen JF, Møller CT, Bill M, Gao Z, Bak RO, Holm K, Sorensen B, Nyegaard M, Luo Y, Hokland P, Stougaard M, Ludvigsen M, Holm CK. Dual intron-targeted CRISPR-Cas9-mediated disruption of the AML RUNX1-RUNX1T1 fusion gene effectively inhibits proliferation and decreases tumor volume in vitro and in vivo. Leukemia 2023; 37:1792-1801. [PMID: 37464068 PMCID: PMC10457201 DOI: 10.1038/s41375-023-01950-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023]
Abstract
Oncogenic fusion drivers are common in hematological cancers and are thus relevant targets of future CRISPR-Cas9-based treatment strategies. However, breakpoint-location variation in patients pose a challenge to traditional breakpoint-targeting CRISPR-Cas9-mediated disruption strategies. Here we present a new dual intron-targeting CRISPR-Cas9 treatment strategy, for targeting t(8;21) found in 5-10% of de novo acute myeloid leukemia (AML), which efficiently disrupts fusion genes without prior identification of breakpoint location. We show in vitro growth rate and proliferation reduction by 69 and 94% in AML t(8;21) Kasumi-1 cells, following dual intron-targeted disruption of RUNX1-RUNX1T1 compared to a non t(8;21) AML control. Furthermore, mice injected with RUNX1-RUNX1T1-disrupted Kasumi-1 cells had in vivo tumor growth reduction by 69 and 91% compared to controls. Demonstrating the feasibility of RUNX1-RUNX1T1 disruption, these findings were substantiated in isolated primary cells from a patient diagnosed with AML t(8;21). In conclusion, we demonstrate proof-of-principle of a dual intron-targeting CRISPR-Cas9 treatment strategy in AML t(8;21) without need for precise knowledge of the breakpoint location.
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Affiliation(s)
- Signe Neldeborg
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Johannes Frasez Soerensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Boe Sorensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Hokland
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Danish Life Science Cluster, Copenhagen, Denmark
| | - Maja Ludvigsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.
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5
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Trier Maansson C, Meldgaard P, Stougaard M, Nielsen AL, Sorensen BS. Cell-free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients. Mol Oncol 2023; 17:722-736. [PMID: 36825535 PMCID: PMC10158780 DOI: 10.1002/1878-0261.13394] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Cell-free DNA (cfDNA) in blood plasma can be bound to nucleosomes that contain post-translational modifications representing the epigenetic profile of the cell of origin. This includes histone H3 lysine 36 trimethylation (H3K36me3), a marker of active transcription. We hypothesised that cell-free chromatin immunoprecipitation (cfChIP) of H3K36me3-modified nucleosomes present in blood plasma can delineate tumour gene expression levels. H3K36me3 cfChIP followed by targeted NGS (cfChIP-seq) was performed on blood plasma samples from non-small-cell lung cancer (NSCLC) patients (NSCLC, n = 8), small-cell lung cancer (SCLC) patients (SCLC, n = 4) and healthy controls (n = 4). H3K36me3 cfChIP-seq demonstrated increased enrichment of mutated alleles compared with normal alleles in plasma from patients with known somatic cancer mutations. Additionally, genes identified to be differentially expressed in SCLC and NSCLC tumours had concordant H3K36me3 cfChIP enrichment profiles in NSCLC (sensitivity = 0.80) and SCLC blood plasma (sensitivity = 0.86). Findings here expand the utility of cfDNA in liquid biopsies to characterise treatment resistance, cancer subtyping and disease progression.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark.,Department of Clinical Medicine, Aarhus University, Denmark.,Department of Biomedicine, Aarhus University, Denmark
| | - Peter Meldgaard
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark.,Department of Oncology, Aarhus University Hospital, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Denmark.,Department of Pathology, Aarhus University Hospital, Denmark
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark.,Department of Clinical Medicine, Aarhus University, Denmark
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6
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Keller JG, Mizielinski K, Petersen KV, Stougaard M, Knudsen BR, Tesauro C. Simple and Fast Rolling Circle Amplification-Based Detection of Topoisomerase 1 Activity in Crude Biological Samples. J Vis Exp 2022. [DOI: 10.3791/64484] [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: 12/05/2022] Open
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7
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Mortensen D, Ulhøi BP, Lukacova S, Alsner J, Stougaard M, Nyengaard JR. Impact of new molecular criteria on diagnosis and survival of adult glioma patients. IBRO Neurosci Rep 2022; 13:299-305. [PMID: 36204252 PMCID: PMC9529576 DOI: 10.1016/j.ibneur.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
The fifth edition WHO classification of Tumors of the Central nervous system (WHO-CNS5) integrated new molecular parameters to refine CNS tumor classification. This study aimed to reclassify a retrospective cohort of adult glioma patients according to WHO-CNS5, and assess if overall survival (OS) correlated with the revised diagnosis. Further, the diagnostic impact of methylation profiling (MP) was evaluated. Adult gliomas diagnosed according to 2016 WHO-CNS (n = 226) were evaluated according to WHO-CNS5 criteria. All patients had diagnostic NGS performed. 29 patients had 850k MP performed due to challenging tumor cases. OS was analyzed using Kaplan-Meier plots and log-rank test. 19 patients were reclassified. Specifically, diffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma (DAG-G) were reclassified as glioblastoma (n = 15). Shifts to glioblastoma were because of TERT promoter (TERTp) mutation (n = 9), EGFR amplification (n = 2), EGFR amplification and TERTp mutation (n = 1), and TERTp mutation with gain of chromosome 7, but uncertain chromosome 10 status due to lack of NGS coverage (n = 3). Lower grade IDH-mutant astrocytomas were reclassified as astrocytoma IDH-mutant, WHO grade 4 due to CDKN2A/B homozygous deletion (n = 4). No significant difference in OS was found for reclassified DAG-G in whole group (p = 0.59) and for TERTp mutation only (p = 0.44), compared to glioblastoma. MP resulted in revised diagnosis (n = 2), confirmed diagnosis (n = 15) and no match (n = 12). Our study showed similar overall survival for glioblastoma and DAG patients, supporting that isolated TERTp mutation may have a prognostic role in IDH-wildtype gliomas. Further, our study suggests MP is useful for confirming the diagnoses in challenging tumors. Retrospective cohort of adult glioma reclassified using WHO-CNS5 molecular criteria. 8.4% of the cohort received a new diagnosis and often a higher WHO grade. TERT promoter mutation suggested as a prognostic factor in IDH wildtype gliomas. DNA methylation profiling useful for diagnostically difficult cases.
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Affiliation(s)
- Danny Mortensen
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
- Correspondence to: Department of Clinical Medicine, Core Center for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Palle Juul Jensens Boulevard 99, C112, Level 1, DK-8200 Aarhus N, Denmark.
| | | | | | - Jan Alsner
- Department of Oncology, Aarhus University Hospital, Denmark
| | | | - Jens Randel Nyengaard
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
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8
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Petersen KV, Tesauro C, Hede MS, Pages C, Marcussen LB, Keller JG, Bugge M, Holm K, Bjergbæk L, Stougaard M, Wejse C, Knudsen BR. Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts. Sensors (Basel) 2022; 22:7763. [PMID: 36298113 PMCID: PMC9608553 DOI: 10.3390/s22207763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The method is based on rolling circle amplification of circular DNA products that can only be formed upon restriction digestion of specially designed DNA substrates. By combining the activity of the target restriction endonuclease with the highly specific Cre recombinase to generate DNA circles, we demonstrate specific detection of selected restriction endonuclease activities even in crude cell extracts. This is, to our knowledge, the first example of a sensor system that allows activity measurements of restriction endonucleases in crude samples. The presented sensor system may prove valuable for future characterization of bacteria species or strains based on their expression of restriction endonucleases as well as for quantification of restriction endonuclease activities directly in extracts from recombinant cells.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
| | | | | | - Camilla Pages
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Josephine Geertsen Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Bugge
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Lotte Bjergbæk
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Christian Wejse
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
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9
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Keller JG, Hymøller KM, Thorsager ME, Hansen NY, Erlandsen JU, Tesauro C, Simonsen AKW, Andersen AB, VandsøPetersen K, Holm LL, Stougaard M, Andresen BS, Kristensen P, Frøhlich R, Knudsen BR. Topoisomerase 1 inhibits MYC promoter activity by inducing G-quadruplex formation. Nucleic Acids Res 2022; 50:6332-6342. [PMID: 35687110 PMCID: PMC9226537 DOI: 10.1093/nar/gkac482] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/28/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
We have investigated the function of human topoisomerase 1 (TOP1) in regulation of G-quadruplex (G4) formation in the Pu27 region of the MYC P1 promoter. Pu27 is among the best characterized G4 forming sequences in the human genome and it is well known that promoter activity is inhibited upon G4 formation in this region. We found that TOP1 downregulation stimulated transcription from a promoter with wildtype Pu27 but not if the G4 motif in Pu27 was interrupted by mutation(s). The effect was not specific to the MYC promoter and similar results were obtained for the G4 forming promoter element WT21. The other major DNA topoisomerases with relaxation activity, topoisomerases 2α and β, on the other hand, did not affect G4 dependent promoter activity. The cellular studies were supported by in vitro investigations demonstrating a high affinity of TOP1 for wildtype Pu27 but not for mutant sequences unable to form G4. Moreover, TOP1 was able to induce G4 formation in Pu27 inserted in double stranded plasmid DNA in vitro. This is the first time TOP1 has been demonstrated capable of inducing G4 formation in double stranded DNA and of influencing G4 formation in cells.
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Affiliation(s)
- Josephine Geertsen Keller
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | | | - Noriko Y Hansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jens Uldum Erlandsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Anne Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark.,Department of Pathology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Peter Kristensen
- Faculty of Engineering and Science, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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10
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Eiset A, Aoun M, Stougaard M, Gottlieb A, Haddad R, Frydenberg M, Naja W. The prevalence of post-traumatic stress disorder in Syrian refugees increased after long-distance migration. Eur Psychiatry 2022. [PMCID: PMC9565903 DOI: 10.1192/j.eurpsy.2022.563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Introduction Refugees are forced migrants but there is a large variation in the distance that refugees cover and there is a knowledge gap on how this may affect refugees’ health and health care needs. Objectives Herein, we investigate the association between long-distance migration and post-traumatic stress disorder (PTSD), a serious psychiatric disorder associated with deteriorating mental and somatic health and highly prevalent in refugees. Methods Included were 712 adult Syrian refugees and asylum seekers in Lebanon and Denmark arriving no more than 12 months prior to inclusion. The Harvard Trauma Questionnaire was used to assess PTSD and the estimate of association was obtained by multiply imputing missing data and adjusting for confounding by propensity score-weighting with covariates age, sex, socioeconomic status, trauma experience, and WHO-5-score, reporting the bootstrap 95-percentile confidence interval (95% CI). Additionally, a number of sensitivity analysis were carried out. Results The prevalence of PTSD was high in both Lebanon (55%) and Denmark (60%) and long-distance migration was associated with a 9 percentage point (95% CI [-1; 19]) increase in the prevalence of PTSD among newly arrived Syrian refugees and asylum-seekers. Conclusions In the present study the prevalence of PTSD increased after long-distance migration which may support considering “long-distance migration” in refugee health screenings and in particular when assessing the risk of post-traumatic stress disorder. This is a first step in examining the health effects of migration on refugee health. Disclosure No significant relationships.
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11
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Lilja-Fischer J, Stougaard M, Kristensen M, Steiniche T, Eriksen J, Overgaard J. MO-0383 A validated prognostic genetic profile independent of smoking in HPV-positive oropharynx cancer. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02349-0] [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: 10/18/2022]
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12
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Simonsen AT, Utke A, Lade-Keller J, Thomsen LW, Steiniche T, Stougaard M. A targeted expression panel for classification, gene fusion detection and PD-L1 measurements - Can molecular profiling replace immunohistochemistry in non-small cell lung cancer? Exp Mol Pathol 2022; 125:104749. [PMID: 35093316 DOI: 10.1016/j.yexmp.2022.104749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/10/2021] [Accepted: 01/22/2022] [Indexed: 11/19/2022]
Abstract
The histological classification of non-small-cell lung cancer (NSCLC) and identification of possible therapeutic targets are important for disease management. However, as biopsies are often small, with a limited amount of tumor cells, it can be challenging to obtain enough tissue for the needed number of diagnostic immunohistochemical stains and molecular analyses. In this study, we combined a small custom designed targeted expression panel with a commercial fusion transcript assay by which we were able to perform both a histological classification (transcribing the expression of the genes encoding TTF1, Napsin A, CK5/6, and the truncated P63 isoform ΔNp63 (p40) into either adenocarcinoma or squamous cell carcinoma) and an identification of fusion genes involving ALK, RET, and ROS1. The expression panel also included the PD-L1 encoding gene, CD274, in order to evaluate the PD-L1 mRNA potential for identification of patients who will benefit from immune checkpoint inhibitor treatment. We evaluated the panel using 42 NSCLC patient samples. The molecular profiling agreed with the original immunohistochemistry (IHC)-based classification in 93% of the cases. For ten of the patients, being fusion gene positive, the fusion transcripts were detected in 100%. The molecular assessment of PD-L1 also showed agreement with the original assessment made by IHC. In conclusion, this study presents a small, targeted expression panel with the potential to perform both a molecularly based histological classification and a fusion gene identification in NSCLC patients as well as identifying PD-L1 status from a very limited amount of starting material.
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Affiliation(s)
| | - Amalie Utke
- Department of Clinical Medicine, Aarhus University, Denmark
| | | | | | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark.
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13
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Eiset AH, Aoun MP, Stougaard M, Gottlieb AG, Haddad RS, Frydenberg M, Naja WJ. The prevalence of post-traumatic stress disorder increased in refugees after long-distance migration. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab165.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] Open
Abstract
Abstract
Background
Refugees are forced migrants but there is a large variation in the distance that refugees cover. This may importantly affect their health needs. Previous studies suggest an inverse association between long-distance migration and self-rated health in the general population, possibly related to difficulty in acculturation but there is a knowledge gap in the health effects of migration in refugee populations. Here, we estimate the association between long-distance migration and post-traumatic stress disorder (PTSD), a severe mental health disorder associated with deteriorating psychiatric and somatic health and highly prevalent in refugees.
Methods
Included were 712 adult Syrian refugees and asylum seekers in Lebanon and Denmark arriving no more than 12 months prior to inclusion. The Harvard Trauma Questionnaire was used to assess PTSD and the estimate of association was obtained by multiply imputing missing data and adjusting for confounding by propensity score-weighting with covariates age, sex, socioeconomic status, trauma experience, and WHO-5-score, reporting the bootstrap 95-percentile confidence interval (CI). Additionally, a number of sensitivity analysis were carried out.
Results
The prevalence of PTSD was high in both Lebanon (55%) and Denmark (60%). After adjusting for biases the prevalence difference increased from 5 percentage point (95-percentile CI [-5; 15] percentage point) to 9 percentage point (95-percentile CI [-1; 19] percentage point). All sensitivity analysis produced estimates of the same direction and magnitude, except when grossly violating the assumption of multiple imputation which halved the magnitude of the association.
Conclusions
We found that long-distance migration was associated with an increase in the prevalence of PTSD among newly arrived Syrian refugees and asylum-seekers. This is a first step in examining the effects of migration in refugee health.
Key messages
Long-distance migration was positively associated with prevalence of post-traumatic stress disorder in Syrian refugees. This is a first step to investigate the impact of migration in refugee health.
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Affiliation(s)
- AH Eiset
- Department of Affective Disorders, Aarhus University Hospital – Psychiatry, Aarhus, Denmark
| | - MP Aoun
- Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - M Stougaard
- Department of Affective Disorders, Aarhus University Hospital – Psychiatry, Aarhus, Denmark
| | - AG Gottlieb
- Department of Affective Disorders, Aarhus University Hospital – Psychiatry, Aarhus, Denmark
| | - RS Haddad
- Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | | | - WJ Naja
- Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
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14
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Petersen KV, Selas A, Hymøller KM, Mizielinski K, Thorsager M, Stougaard M, Alonso C, Palacios F, Pérez-Pertejo Y, Reguera RM, Balaña-Fouce R, Knudsen BR, Tesauro C. Simple and Fast DNA Based Sensor System for Screening of Small-Molecule Compounds Targeting Eukaryotic Topoisomerase 1. Pharmaceutics 2021; 13:1255. [PMID: 34452216 PMCID: PMC8401307 DOI: 10.3390/pharmaceutics13081255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Eukaryotic topoisomerase 1 is a potential target of anti-parasitic and anti-cancer drugs. Parasites require topoisomerase 1 activity for survival and, consequently, compounds that inhibit topoisomerase 1 activity may be of interest. All effective topoisomerase 1 drugs with anti-cancer activity act by inhibiting the ligation reaction of the enzyme. Screening for topoisomerase 1 targeting drugs, therefore, should involve the possibility of dissecting which step of topoisomerase 1 activity is affected. Methods: Here we present a novel DNA-based assay that allows for screening of the effect of small-molecule compounds targeting the binding/cleavage or the ligation steps of topoisomerase 1 catalysis. This novel assay is based on the detection of a rolling circle amplification product generated from a DNA circle resulting from topoisomerase 1 activity. Results: We show that the binding/cleavage and ligation reactions of topoisomerase 1 can be investigated separately in the presented assay termed REEAD (C|L) and demonstrate that the assay can be used to investigate, which of the individual steps of topoisomerase 1 catalysis are affected by small-molecule compounds. The assay is gel-free and the results can be detected by a simple colorimetric readout method using silver-on-gold precipitation rendering large equipment unnecessary. Conclusion: REEAD (C|L) allows for easy and quantitative investigations of topoisomerase 1 targeting compounds and can be performed in non-specialized laboratories.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark;
| | - Asier Selas
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Kirstine Mejlstrup Hymøller
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
| | | | - Maria Thorsager
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark;
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Concepcion Alonso
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Francisco Palacios
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Yolanda Pérez-Pertejo
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Rosa M. Reguera
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Rafael Balaña-Fouce
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
| | - Cinzia Tesauro
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
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15
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Tønnesen E, Lade-Keller J, Stougaard M. Frequently used quantitative polymerase chain reaction-based methods overlook potential clinically relevant genetic alterations in epidermal growth factor receptor compared with next-generation sequencing: a retrospective clinical comparison of 1839 lung adenocarcinomas. Hum Pathol 2021; 115:67-75. [PMID: 34153308 DOI: 10.1016/j.humpath.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
AIMS The aim of the study was to investigate the advantage of implementing next-generation sequencing (NGS) compared with quantitative polymerase chain reaction (qPCR) when performing routine molecular diagnostics in adenocarcinomas of the lung. METHODS The study is a retrospective cross-sectional observational study of 1839 cytological and histological adenocarcinoma biopsies investigated for gene mutations from 2016 to 2018 at the Department of Pathology at Aarhus University Hospital. A total of 1169 samples were analyzed by qPCR for the presence of EGFR hotspot mutations from 2016 to 2017. A total of 670 samples were analyzed with NGS for the presence of EGFR mutations and other gene mutations in 2018. RESULTS The average frequency of EGFR mutations in the study population was 11.5%, with the highest frequency found in 2018, where NGS was implemented (10.8% in 2016, 11.5% in 2017, and 12.2% in 2018). Possible therapy resistance markers such as EGFR exon 20 mutations were found more commonly after NGS implementation, the difference being statistically significant (P = .015). In addition, NGS (2018) showed that 40.6% of the samples had KRAS mutations and 6.0% had BRAF mutations, mutations not commonly investigated in lung adenocarcinomas when qPCR is the method of choice. Among the EGFR-mutated samples analyzed with NGS, 13 contained a concurrent EGFR mutation, whereas three and two contained a concurrent KRAS and BRAF mutations, respectively. CONCLUSIONS With the implementation in a clinical setting, NGS identifies more uncommon but potentially clinically important EGFR mutations, unique combinations of EGFR mutations, and concurrent mutations in KRAS and BRAF.
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Affiliation(s)
- Ea Tønnesen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark.
| | - Johanne Lade-Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark
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16
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Bobach IS, Stougaard M. SNP-based detection of allelic imbalance: A novel approach for identifying KIAA1549-BRAF fusion in pilocytic astrocytoma using DNA sequencing. Exp Mol Pathol 2021; 120:104621. [PMID: 33626378 DOI: 10.1016/j.yexmp.2021.104621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/19/2022]
Abstract
Pilocytic astrocytoma (PA) is the most common glioma subtype found in children, and it is a non-malignant tumor type. The majority of PAs is caused by an approximately 2 Mb tandem duplication within 7q34 which creates an in-frame KIAA1549-BRAF fusion gene. The kinase domain of BRAF is fused to the N-terminal of KIAA1549, whereby BRAF is constitutively activated. We here present a novel approach for identifying KIAA1549-BRAF fusion based on single nucleotide polymorphism (SNP) analysis and next generation sequencing (NGS). Highly polymorphic SNPs in the duplicated area and in adjacent areas were selected and a custom targeted amplicon based NGS panel was designed. The panel was tested on DNA extracted from formalin fixed and paraffin embedded tissue from a retrospective cohort, consisting of biopsies from patients with PA, anaplastic astrocytoma, oligodendroglioma and glioblastoma as well as two non-tumor biopsies. The panel could distinguish chromosome 7 gain from BRAF fusion and correctly identified 8/9 PA samples with KIAA1549-BRAF fusion confirmed by RNA sequencing. The one biopsy where no fusion was detected was fresh frozen and from the RNA sequencing expected to have very low tumor content. No allelic imbalance was detected in either oligodendroglioma or in the non-tumor biopsies.
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Affiliation(s)
- Ida Schwartz Bobach
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Pathology, Aarhus University Hospital, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Pathology, Aarhus University Hospital, Denmark.
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17
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Lippert J, Bønløkke S, Utke A, Knudsen BR, Sorensen BS, Steiniche T, Stougaard M. Targeted next generation sequencing panel for HPV genotyping in cervical cancer. Exp Mol Pathol 2020; 118:104568. [PMID: 33171155 DOI: 10.1016/j.yexmp.2020.104568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
Cervical cancer are generally caused by a persistent infection with the oncogenic virus, HPV. Patients with HPV integration are more prone to develop cervical cancer than patients without integration. In this proof-of-concept study, we aimed to develop a sensitive method based on targeted amplicon based NGS for early and precise detection of high-risk HPV-genotypes that are highly associated with the development of cervical cancer. Furthermore, we aimed to investigate if amplicon based NGS allowed for HPV genotyping in cervical lesions and whether it could detect HPV integration. The cohort included a group of CIN3+ biopsies (n = 64), CIN2 samples that progressed (n = 5), CIN2 samples that regressed (n = 3), healthy controls (n = 10), and plasma samples (n = 10) from cervical cancer patients. Sequencing was performed using a custom targeted NGS panel designed to detect all 25 high-risk and probably high-risk and two low-risk HPV genotypes. The method was validated by the SPF10 PCR-DEIA-LiPA25 assay. In the cohort, the following HPV genotypes were identified: HPV-16, 18, 31, 33, 35, 45, 51, 52, 56, 58, and 59. When comparing the results from the SPF10 PCR-DEIA-LiPA25 analyses with the NGS analyses, there was close to a perfect agreement (K = 0.92) among the genotyped HPV types, while in the two cases with complete disagreement, a third assay was applied, and here the results of the NGS analyses were confirmed. Whereas multiple HPV types were detected by the SPF10 PCR-DEIA-LiPA25 assay, the NGS analysis clearly suggest that there is one predomentant HPV type. The NGS assay was capable of detecting HPV-16 in a previous false-negative sample classified by the INNO-LiPA assay, emphasizing the importance of including multiple regions of the HPV genome when genotyping. For the 10 plasma samples, our NGS analyses showed full agreement with the digital droplet PCR (ddPCR) analyses of HPV positive as well as negative plasma samples. Lastly, the custom panel was capable of detecting the integration of HPV-16 in the SiHa cell line. The HPV panel provides a highly cost-effective method for HPV detection and genotyping, as exemplified by a list price of around 75 € per sample. In conclusion, the current study demonstrates that targeted NGS is capable of detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides for early diagnosis and prognosis of cervical cancer disease progression, thereby optimizing the potential of recovery and survival for these patients.
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Affiliation(s)
- J Lippert
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark
| | - S Bønløkke
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark
| | - A Utke
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark
| | - B R Knudsen
- Aarhus University, Department of Molecular Biology and Genetics, Aarhus, Denmark
| | - B S Sorensen
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Clinical Biochemistry, Aarhus, Denmark
| | - T Steiniche
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark
| | - M Stougaard
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark.
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18
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Tesauro C, Simonsen AK, Andersen MB, Petersen KW, Kristoffersen EL, Algreen L, Hansen NY, Andersen AB, Jakobsen AK, Stougaard M, Gromov P, Knudsen BR, Gromova I. Topoisomerase I activity and sensitivity to camptothecin in breast cancer-derived cells: a comparative study. BMC Cancer 2019; 19:1158. [PMID: 31783818 PMCID: PMC6884793 DOI: 10.1186/s12885-019-6371-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
Background Camptothecin (CPT) and its derivatives are currently used as second- or third-line treatment for patients with endocrine-resistant breast cancer (BC). These drugs convert nuclear enzyme DNA topoisomerase I (TOP1) to a cell poison with the potential to damage DNA by increasing the half-life of TOP1-DNA cleavage complexes (TOP1cc), ultimately resulting in cell death. In small and non-randomized trials for BC, researchers have observed extensive variation in CPT response rates, ranging from 14 to 64%. This variability may be due to the absence of reliable selective parameters for patient stratification. BC cell lines may serve as feasible models for generation of functional criteria that may be used to predict drug sensitivity for patient stratification and, thus, lead to more appropriate applications of CPT in clinical trials. However, no study published to date has included a comparison of multiple relevant parameters and CPT response across cell lines corresponding to specific BC subtypes. Method We evaluated the levels and possible associations of seven parameters including the status of the TOP1 gene (i.e. amplification), TOP1 protein expression level, TOP1 activity and CPT susceptibility, activity of the tyrosyl-DNA phosphodiesterase 1 (TDP1), the cellular CPT response and the cellular growth rate across a representative panel of BC cell lines, which exemplifies three major BC subtypes: Luminal, HER2 and TNBC. Results In all BC cell lines analyzed (without regard to subtype classification), we observed a significant overall correlation between growth rate and CPT response. In cell lines derived from Luminal and HER2 subtypes, we observed a correlation between TOP1 gene copy number, TOP1 activity, and CPT response, although the data were too limited for statistical analyses. In cell lines representing Luminal and TNBC subtypes, we observed a direct correlation between TOP1 protein abundancy and levels of enzymatic activity. In all three subtypes (Luminal, HER2, and TNBC), TOP1 exhibits approximately the same susceptibility to CPT. Of the three subtypes examined, the TNBC-like cell lines exhibited the highest CPT sensitivity and were characterized by the fastest growth rate. This indicates that breast tumors belonging to the TNBC subtype, may benefit from treatment with CPT derivatives. Conclusion TOP1 activity is not a marker for CPT sensitivity in breast cancer.
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Affiliation(s)
- Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anne Katrine Simonsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Present Address: Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Marie Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Emil Laust Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Present Address: MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Line Algreen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anne Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Pavel Gromov
- Genome Integrity Unit, Breast Cancer Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Irina Gromova
- Genome Integrity Unit, Breast Cancer Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark.
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19
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Lilja-Fischer JK, Saksø M, Stougaard M, Steiniche T, Overgaard J. Distinguishing recurrence and new primary tumor as well as the origin of neck metastases in head and neck cancer clinical trials by targeted DNA sequencing. Acta Oncol 2019; 58:1506-1508. [PMID: 31271080 DOI: 10.1080/0284186x.2019.1629015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jacob Kinggaard Lilja-Fischer
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
- Department of Otorhinolaryngology – Head and Neck Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Saksø
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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20
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Lilja-Fischer JK, Ulhøi BP, Alsner J, Stougaard M, Thomsen MS, Busk M, Lassen P, Steiniche T, Nielsen VE, Overgaard J. Characterization and radiosensitivity of HPV-related oropharyngeal squamous cell carcinoma patient-derived xenografts. Acta Oncol 2019; 58:1489-1494. [PMID: 31510843 DOI: 10.1080/0284186x.2019.1660802] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Oropharyngeal squamous cell carcinomas (OPSCC) are rising rapidly in incidence due to Human Papillomavirus (HPV) and/or tobacco smoking. Prognosis is better for patients with HPV-positive disease, but may also be influenced by tobacco smoking and other factors. There is a need to individualize treatment to minimize morbidity and improve prognosis. Patient-derived xenografts (PDX) is an emerging pre-clinical research model that may more accurately reflect the human disease, and is an attractive platform to study disease biology and develop treatments and biomarkers. In this study we describe the establishment of PDX models, compare PDX tumors to the human original, and assess the suitability of this model for radiotherapy research and biomarker development. Material and methods: Tumor biopsies from 34 patients with previously untreated OPSCC were implanted in immunodeficient mice, giving rise to 12 squamous cell carcinoma PDX models (7 HPV+, 5 HPV-). Primary and PDX tumors were characterized extensively, examining histology, immunohistochemistry, cancer gene sequencing and gene expression analysis. Radiosensitivity was assessed in vivo in a growth delay assay. Results: Established PDX models maintained histological and immunohistochemical characteristics as well as HPV-status of the primary tumor. Important cancer driver gene mutations, e.g., in TP53, PIK3CA and others, were preserved. Gene expression related to cancer stem cell markers and gene expression subtype were preserved, while gene expression related to hypoxia and immune response differed. Radiosensitivity studies showed high concordance with clinical observations. Conclusion: PDX from OPSCC preserves important molecular characteristics of the human primary tumor. Radiosensitivity were in accordance with clinically observed treatment response. The PDX model is a clinically relevant surrogate model of head and neck cancer. Perspectives include increased understanding of disease biology, which could lead to development of novel treatments and biomarkers.
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Affiliation(s)
- Jacob Kinggaard Lilja-Fischer
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Denmark
- Department of Otorhinolaryngology – Head and Neck Surgery, Aarhus University Hospital, Denmark
| | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Denmark
| | | | | | - Morten Busk
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Denmark
| | - Pernille Lassen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Denmark
- Department of Oncology, Aarhus University Hospital, Denmark
| | | | | | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Denmark
- Department of Oncology, Aarhus University Hospital, Denmark
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21
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Hojbjerg JA, Madsen AT, Schmidt HH, Sorensen SF, Stougaard M, Meldgaard P, Sorensen BS. Intra-individual variation of circulating tumour DNA in lung cancer patients. Mol Oncol 2019; 13:2098-2106. [PMID: 31306545 PMCID: PMC6763781 DOI: 10.1002/1878-0261.12546] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Circulating tumour DNA (ctDNA) has been increasingly incorporated into the treatment of cancer patients. ctDNA is generally accepted as a powerful diagnostic tool, whereas the utility of ctDNA to monitor disease activity needs to be fully validated. Central to this challenge is the question of whether changes in longitudinal ctDNA measurements reflect disease activity or merely biological variation. Thus, the aim of this study was to explore the intra‐individual biological variation of ctDNA in lung cancer patients. We identified tumour‐specific mutations using next‐generation sequencing. Day‐to‐day and hour‐to‐hour variations in plasma concentrations of the mutant allele and wild‐type cell‐free DNA (cfDNA) were determined using digital PCR. The levels of the mutant alleles varied by as much as 53% from day to day and 27% from hour to hour. cfDNA varied up to 19% from day to day and up to 56% from hour to hour, as determined using digital PCR. Variations were independent of the concentration. Both mutant allele concentrations and wild‐type cfDNA concentrations showed considerable intra‐individual variation in lung cancer patients with nonprogressive disease. This pronounced biological variation of the circulating DNA should be investigated further to determine whether ctDNA can be used for monitoring cancer activity.
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Affiliation(s)
- Johanne A Hojbjerg
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | - Anne T Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | - Steffen F Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | | | - Boe S Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
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Pauwels P, Steiniche T, Gazin M, Van de Velde J, Bellon E, Rondelez E, Vandenbroeck L, Zwaenepoel K, De Winne K, Meyer T, Mejer J, Stougaard M, Decanniere K, Devogelaere B, Maertens GG, De Craene B. The Idylla MSI Test (CE-IVD) multi-center concordance study: Microsatellite instability detection in colorectal cancer samples. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e15112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15112 Background: To validate the Idylla MSI Test to detect microsatellite instability (MSI) in colorectal cancer (CRC) samples in comparison with Promega MSI Analysis System v1.2 (Promega MSI) and in conditions similar to normal use. Methods: The study was performed on residual formalin-fixed and paraffin-embedded (FFPE) samples obtained from routine diagnostics by two centers, University Hospital Aarhus and University Hospital Antwerp. Samples originated from CRC patients (all stages). Both centers performed the Idylla MSI Test (with 7 novel homopolymer deletion markers) at their premises on 150 and 180 samples, respectively. The comparator method, Promega MSI, was performed for all 330 samples by University Hospital Antwerp. Results: Seven (n=7) of 330 samples were excluded from the concordance analysis due to invalid or error (failed) results for Idylla MSI Test and/or Promega MSI. For the 323 valid results, overall, positive and negative percentage agreement were 99.7% (98.3%-100%;), 98.7% (92.9%-99.8%) and 100% (98.5%-100%), respectively. A higher number of invalids was observed for Promega MSI (2.1%) compared to the Idylla MSI Test (0.6%) taking into account per protocol retesting (18 retests for Promega MSI (6%) and 3 for Idylla MSI Test (1%)). Conclusions: This study validated the Idylla MSI Test with high performance and low invalid rate to discriminate MSI-H from MSS status on a clinical routine set of CRC samples.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tine Meyer
- Aarhus University Hospital, Aarhus, Denmark
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23
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Lilja-Fischer J, Ulhøi B, Stougaard M, Lassen P, Steniche T, Alsner J, Overgaard J. PO-101 HPV, tobacco smoking and specific mutations and amplifications in oropharyngeal cancer. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)30267-1] [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: 11/25/2022]
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24
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Franch O, Han X, Marcussen LB, Givskov A, Andersen MB, Godbole AA, Harmsen C, Nørskov-Lauritsen N, Thomsen J, Pedersen FS, Wang Y, Shi D, Wejse C, Pødenphant L, Nagaraja V, Bertl J, Stougaard M, Ho YP, Hede MS, Labouriau R, Knudsen BR. A new DNA sensor system for specific and quantitative detection of mycobacteria. Nanoscale 2019; 11:587-597. [PMID: 30556557 DOI: 10.1039/c8nr07850e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.
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Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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25
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Abstract
CRISPR/Cas9 is a powerful genetic engineering technology that enables the introduction of genomic changes such as deletions and insertions of specific bits of DNA in cells with high precision. Compared to other programmable DNA nuclease such as ZFNs and TALENs, the specific binding of the Cas9 nuclease is mediated by a small guide RNA (gRNA), which can easily be designed to target any locus in the genome. The ease of generating novel gRNA vectors and its high efficiency has rapidly made CRISPR-Cas9 the dominant tool in gene editing applications, including gene knockout, knockin, tagging, etc. Here we describe our method for rapid and efficient generation of gene knockout or deletion cells using CRISPR/Cas9 within the time span of one month. The design of gRNAs, plasmid cloning, transfection, cell culturing, positive clone selection, and screening can be obtained from this method.
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Affiliation(s)
- Signe Neldeborg
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- BGI-Shenzhen, Shenzhen, China.
- BGI-Qingdao, Qingdao, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
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26
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Lade-Keller J, Yuusufi S, Riber-Hansen R, Steiniche T, Stougaard M. Telomerase reverse transcriptase promoter mutations and solar elastosis in cutaneous melanoma. Melanoma Res 2018; 28:398-409. [PMID: 29570169 DOI: 10.1097/cmr.0000000000000446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The aims of this study were to assess the prognostic potential of solar elastosis grading and telomerase reverse transcriptase (TERT) promoter mutations (TERTp) in melanoma and to evaluate whether an association between solar elastosis and TERTp exists. Solar elastosis in the dermis was evaluated in hematoxylin and eosin-stained whole slides from 486 malignant melanomas. Pyrosequencing was used to detect TERTp in 189 samples. There was no association between solar elastosis and TERTp (P=0.3). Severe elastosis was associated with older age (P<0.0001), ulceration (P=0.03), and location in the head/neck region (P<0.0001). The absence of elastosis was associated with younger age (P<0.0001), benign nevus remnants (P=0.001), and a positive BRAF V600E expression (P<0.0001). Severe elastosis predicted a worse relapse-free survival (hazard ratio: 2.18; 95% confidence interval: 1.30-3.64; P=0.003). However, it was not independent of age. TERTp was not associated with any adverse prognostic or clinicopathological outcome, nor any mitogen-activated protein kinase-related protein expressions. However, at a cutoff corresponding to the sensitivity of Sanger sequencing, TERTp predicted melanoma-specific death independently of age, and was associated with Breslow thickness, ulceration, tumor stage at diagnosis, BRAF V600E oncoprotein, and absence of p16 expression. In conclusion, TERTp were not related to severe elastosis and may thus be triggered by both chronic and acute intermittent sun exposure, the latter not visible on ordinary hematoxylin and eosin-stained slides. Neither TERTp nor severe elastosis predicted an adverse outcome in melanoma. An absence of elastosis was seen in younger melanoma patients and may be used to select those melanomas originating in a nevus, which often harbors a BRAF mutation.
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27
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Lilja-Fischer J, Ulhøi B, Alsner J, Stougaard M, Thomsen M, Lassen P, Steiniche T, Nielsen V, Overgaard J. Characterization and Radiosensitivity of HPV-Related Oropharyngeal Squamous Cell Carcinoma Patient-Derived Xenografts. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2017.12.172] [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: 11/16/2022]
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28
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Lilja-Fischer J, Ulhøi B, Alsner J, Stougaard M, Lassen P, Steiniche T, Overgaard J. Impact of Tobacco Smoking on Mutational Landscape in HPV-Associated Oropharyngeal Cancer. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2017.12.301] [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: 11/17/2022]
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29
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Hede MS, Fjelstrup S, Lötsch F, Zoleko RM, Klicpera A, Groger M, Mischlinger J, Endame L, Veletzky L, Neher R, Simonsen AKW, Petersen E, Mombo-Ngoma G, Stougaard M, Ho YP, Labouriau R, Ramharter M, Knudsen BR. Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker. Sci Rep 2018. [PMID: 29515150 PMCID: PMC5841400 DOI: 10.1038/s41598-018-22378-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite. Subsequent rolling circle amplification of the generated DNA circle in the presence of biotin conjugated deoxynucleotides resulted in long tandem repeat products that was visualized colorimetrically upon binding of horse radish peroxidase (HRP) and addition of 3,3′,5,5′-Tetramethylbenzidine that was converted to a blue colored product by HRP. The assay was directly quantitative, specific for Plasmodium parasites, and allowed detection of Plasmodium infection in a single drop of saliva from 35 out of 35 infected individuals tested. The results could be determined directly by the naked eye and documented by quantifying the color intensity using a standard paper scanner.
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Affiliation(s)
| | - Søren Fjelstrup
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
| | - Felix Lötsch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Anna Klicpera
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Johannes Mischlinger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Lilian Endame
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Luzia Veletzky
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Ronja Neher
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | | | - Eskild Petersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Infectious Diseases, The Royal Hospital, Muscat, Oman
| | - Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Magnus Stougaard
- Department of Clinical Medicine, University of Aarhus, Aarhus, Denmark
| | - Yi-Ping Ho
- Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | | | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark.
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30
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Kjeldsen E, Nielsen CJF, Roy A, Tesauro C, Jakobsen AK, Stougaard M, Knudsen BR. Characterization of Camptothecin-induced Genomic Changes in the Camptothecin-resistant T-ALL-derived Cell Line CPT-K5. Cancer Genomics Proteomics 2018; 15:91-114. [PMID: 29496689 PMCID: PMC5892604 DOI: 10.21873/cgp.20068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 11/17/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022] Open
Abstract
Acquisition of resistance to topoisomerase I (TOP1)-targeting camptothecin (CPT) derivatives is a major clinical problem. Little is known about the underlying chromosomal and genomic mechanisms. We characterized the CPT-K5 cell line expressing mutant CPT-resistant TOP1 and its parental T-cell derived acute lymphoblastic leukemia CPT-sensitive RPMI-8402 cell line by karyotyping and molecular genetic methods, including subtractive oligo-based array comparative genomic hybridization (soaCGH) analysis. Karyotyping revealed that CPT-K5 cells had acquired additional structural aberrations and a reduced modal chromosomal number compared to RPMI-8402. soaCGH analysis identified vast copy number alterations and >200 unbalanced DNA breakpoints distributed unevenly across the chromosomal complement in CPT-K5. In addition, the short tandem repeat alleles were found to be highly different between CPT-K5 and its parental cell line. We identified copy number alterations affecting genes important for maintaining genome integrity and reducing CPT-induced DNA damage. We show for the first time that short tandem repeats are targets for TOP1 cleavage, that can be differentially stimulated by CPT.
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Affiliation(s)
- Eigil Kjeldsen
- Cancer Cytogenetics Section, HemoDiagnostic Laboratory, Aarhus University Hospital, Aarhus, Denmark
| | - Christine J F Nielsen
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | - Amit Roy
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | | | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
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31
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Kristoffersen EL, Givskov A, Jørgensen LA, Jensen PW, W Byl JA, Osheroff N, Andersen AH, Stougaard M, Ho YP, Knudsen BR. Interlinked DNA nano-circles for measuring topoisomerase II activity at the level of single decatenation events. Nucleic Acids Res 2017; 45:7855-7869. [PMID: 28541438 PMCID: PMC5570003 DOI: 10.1093/nar/gkx480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/22/2017] [Indexed: 12/23/2022] Open
Abstract
DNA nano-structures present appealing new means for monitoring different molecules. Here, we demonstrate the assembly and utilization of a surface-attached double-stranded DNA catenane composed of two intact interlinked DNA nano-circles for specific and sensitive measurements of the life essential topoisomerase II (Topo II) enzyme activity. Topo II activity was detected via the numeric release of DNA nano-circles, which were visualized at the single-molecule level in a fluorescence microscope upon isothermal amplification and fluorescence labeling. The transition of each enzymatic reaction to a micrometer sized labeled product enabled quantitative detection of Topo II activity at the single decatenation event level rendering activity measurements in extracts from as few as five cells possible. Topo II activity is a suggested predictive marker in cancer therapy and, consequently, the described highly sensitive monitoring of Topo II activity may add considerably to the toolbox of individualized medicine where decisions are based on very sparse samples.
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Affiliation(s)
- Emil L Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
| | - Asger Givskov
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Line A Jørgensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Pia W Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Anni H Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark.,Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
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32
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Keller JG, Tesauro C, Coletta A, Graversen AD, Ho YP, Kristensen P, Stougaard M, Knudsen BR. On-slide detection of enzymatic activities in selected single cells. Nanoscale 2017; 9:13546-13553. [PMID: 28872165 DOI: 10.1039/c7nr05125e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With increasing recognition of the importance in addressing cell-to-cell heterogeneity for the understanding of complex biological systems, there is a growing need for assays capable of single cell analyses. In the current study, we describe the measurement of human topoisomerase I activity in single CD44 positive Caco2 cells specifically captured from a mixed population on glass slides, which were dual functionalized with anti-CD44-antibodies and specific DNA primers. On-slide lysis of captured CD44 positive cells, resulted in the release of human topoisomerase I, allowing the enzyme to circularize a specific linear DNA substrate added to the slides. The generated circles hybridized to the anchored DNA primers and acted as templates for a solid support rolling circle amplification reaction leading to the generation of long tandem repeat products that were detected at the single molecule level in a fluorescent microscope upon hybridization of fluorescent labelled probes. The on-slide detection system was demonstrated to be directly quantitative and specific towards CD44 positive cells. Moreover, it allowed reproducible detection of human topoisomerase I activity in single cells.
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Affiliation(s)
- Josephine Geertsen Keller
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg. 1131, Aarhus University, 8000 Aarhus C, Denmark.
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. Nanoscale 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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Wang J, Liu J, Thomsen J, Selnihhin D, Hede MS, Kirsebom FCM, Franch O, Fjelstrup S, Stougaard M, Ho YP, Pedersen FS, Knudsen BR. Novel DNA sensor system for highly sensitive and quantitative retrovirus detection using virus encoded integrase as a biomarker. Nanoscale 2017; 9:440-448. [PMID: 27934981 DOI: 10.1039/c6nr07428f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the current study we describe a novel DNA sensor system that allows the detection of single catalytic DNA integration events mediated by retrovirus encoded integrase (IN) present in viral particles. This is achieved by rolling circle amplification mediated conversion of enzymatic reactions happening within nanometer dimensions to directly detectable micrometer sized DNA products. The system utilizes the unique integration reaction of IN to generate a surface anchored nicked DNA circle that serves as a substrate for rolling circle amplification and allows for specific, quantitative and sensitive detection of purified recombinant IN or virus particles with a detection limit of less than 30 virus particles per μL of sample. Moreover, by modifying the nucleotide sequences of the utilized DNA it was possible to tailor the system to distinguish between the highly pathogenic lentivirus HIV and the gammaretrovirus murine leukemia virus present in a given sample. Infections with HIV remain a major threat to global health with more than 2 million new infections and 1 million deaths each year. The sensitive and specific detection of HIV particles based on IN activity holds promise for the development of a new type of diagnostic tools suitable for early (within hours of infection) detection of HIV, which would be valuable for prevention strategies as well as for efficient treatment.
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Affiliation(s)
- Jing Wang
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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35
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Viuff D, Antunes F, Evans L, Cameron J, Dyrnesli H, Thue Ravn B, Stougaard M, Thiam K, Andersen B, Kjærulff S, Howard KA. Generation of a double transgenic humanized neonatal Fc receptor (FcRn)/albumin mouse to study the pharmacokinetics of albumin-linked drugs. J Control Release 2016; 223:22-30. [DOI: 10.1016/j.jconrel.2015.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/09/2015] [Accepted: 12/12/2015] [Indexed: 12/31/2022]
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Jandu H, Aluzaite K, Fogh L, Thrane SW, Noer JB, Proszek J, Do KN, Hansen SN, Damsgaard B, Nielsen SL, Stougaard M, Knudsen BR, Moreira J, Hamerlik P, Gajjar M, Smid M, Martens J, Foekens J, Pommier Y, Brünner N, Schrohl AS, Stenvang J. Molecular characterization of irinotecan (SN-38) resistant human breast cancer cell lines. BMC Cancer 2016; 16:34. [PMID: 26801902 PMCID: PMC4722663 DOI: 10.1186/s12885-016-2071-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Background Studies in taxane and/or anthracycline refractory metastatic breast cancer (mBC) patients have shown approximately 30 % response rates to irinotecan. Hence, a significant number of patients will experience irinotecan-induced side effects without obtaining any benefit. The aim of this study was to lay the groundwork for development of predictive biomarkers for irinotecan treatment in BC. Methods We established BC cell lines with acquired or de novo resistance to SN-38, by exposing the human BC cell lines MCF-7 and MDA-MB-231 to either stepwise increasing concentrations over 6 months or an initial high dose of SN-38 (the active metabolite of irinotecan), respectively. The resistant cell lines were analyzed for cross-resistance to other anti-cancer drugs, global gene expression, growth rates, TOP1 and TOP2A gene copy numbers and protein expression, and inhibition of the breast cancer resistance protein (ABCG2/BCRP) drug efflux pump. Results We found that the resistant cell lines showed 7–100 fold increased resistance to SN-38 but remained sensitive to docetaxel and the non-camptothecin Top1 inhibitor LMP400. The resistant cell lines were characterized by Top1 down-regulation, changed isoelectric points of Top1 and reduced growth rates. The gene and protein expression of ABCG2/BCRP was up-regulated in the resistant sub-lines and functional assays revealed BCRP as a key mediator of SN-38 resistance. Conclusions Based on our preclinical results, we suggest analyzing the predictive value of the BCRP in breast cancer patients scheduled for irinotecan treatment. Moreover, LMP400 should be tested in a clinical setting in breast cancer patients with resistance to irinotecan. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2071-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haatisha Jandu
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Kristina Aluzaite
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Louise Fogh
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Sebastian Wingaard Thrane
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Julie B Noer
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Joanna Proszek
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000, Aarhus C, Denmark.
| | - Khoa Nguyen Do
- DTU Multiassay Core (DMAC), Technical University of Denmark, Kemitorvet Building 208, DK-2800, Lyngby, Denmark.
| | - Stine Ninel Hansen
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Britt Damsgaard
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Signe Lykke Nielsen
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000, Aarhus C, Denmark.
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000, Aarhus C, Denmark.
| | - José Moreira
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Petra Hamerlik
- Brain Tumor Biology, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Madhavsai Gajjar
- Brain Tumor Biology, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Marcel Smid
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands.
| | - John Martens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands.
| | - John Foekens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands.
| | - Yves Pommier
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Developmental Therapeutics Branch and Laboratory of Molecular, Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD, 20892-4255, USA.
| | - Nils Brünner
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Anne-Sofie Schrohl
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Strandboulevarden 49, DK-2100, Copenhagen, Denmark.
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Kristoffersen EL, Jørgensen LA, Franch O, Etzerodt M, Frøhlich R, Bjergbæk L, Stougaard M, Ho YP, Knudsen BR. Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations. Nanoscale 2015; 7:9825-9834. [PMID: 25963854 DOI: 10.1039/c5nr01474c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.
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Jakobsen AK, Lauridsen KL, Samuel EB, Proszek J, Knudsen BR, Hager H, Stougaard M. Correlation between topoisomerase I and tyrosyl-DNA phosphodiesterase 1 activities in non-small cell lung cancer tissue. Exp Mol Pathol 2015; 99:56-64. [PMID: 25987486 DOI: 10.1016/j.yexmp.2015.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/04/2015] [Accepted: 05/14/2015] [Indexed: 12/29/2022]
Abstract
Topoisomerase I (TOP1) regulates DNA topology during replication and transcription whereas tyrosyl-DNA phosphodiesterase 1 (TDP1) is involved in the repair of several types of DNA damages, including damages from defective TOP1 catalysis. TOP1 is the target of chemotherapeutic drugs of the camptothecin family (CPT). TDP1 has in cell line based assays been shown to counteract the effect of CPT. We have quantified the enzymatic activities of TOP1 and TDP1 in paired (tumor and adjacent non-tumor) samples from non-small cell lung cancer (NSCLC) patients and show that in NSCLC TOP1 and TDP1 activities are significantly upregulated in the tumor tissue. Furthermore, we found a positive correlation between the TDP1 activity and the tumor percentage (TOP1 activity did not correlate with the tumor percentage) as well as between the activities of TOP1 and TDP1 both within the tumor and the non-tumor group. That TDP1 activity was upregulated in all tumor samples and correlated with the tumor percentage suggest that it must play a highly important function in NSCLC. This could be to protect against TOP1 mediated DNA damage as the activity of TOP1 likewise was upregulated in the majority of tumor samples and correlated positively to the TDP1 activity. Regardless, the finding that the TOP1 and TDP1 activities are upregulated and correlate positively suggests that combinatorial treatment targeting both activities could be advantageous in NSCLC.
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Affiliation(s)
| | | | | | - Joanna Proszek
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Henrik Hager
- Department of Pathology, Aarhus University Hospital, Denmark; Department of Clinical Pathology, Vejle Hospital, Denmark
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Joergensen MW, Labouriau R, Hindkjaer J, Stougaard M, Kolevraa S, Bolund L, Agerholm IE, Sunde L. The parental origin correlates with the karyotype of human embryos developing from tripronuclear zygotes. Clin Exp Reprod Med 2015; 42:14-21. [PMID: 25874169 PMCID: PMC4390676 DOI: 10.5653/cerm.2015.42.1.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 12/29/2014] [Accepted: 01/19/2015] [Indexed: 11/12/2022] Open
Abstract
Objective It has previously been suggested that embryos developing from intracytoplasmic sperm-injected (ICSI) zygotes with three pronuclei (3PN) are endowed with a mechanism for self-correction of triploidy to diploidy. 3PN are also observed in zygotes after conventional in vitro fertilization (IVF). The parental origin, however, differs between the two fertilization methods. Whereas the vast majority of 3PN IVF zygotes are of dispermic origin and thus more likely to have two centrioles, the 3PN ICSI zygotes are digynic in origin and therefore, more likely to have one centriole. In the present study, we examine whether the parental origin of 3PN embryos correlates with the karyotype. Methods The karyotype of each nucleus was estimated using four sequential fluorescence in situ hybridizations-each with two probes-resulting in quantitative information of 8 different chromosomes. The karyotypes were then compared and correlated to the parental origin. Results 3PN ICSI embryos displayed a significantly larger and more coordinated reduction from the assumed initial 3 sets of chromosomes than 3PN IVF embryos. Conclusion The differences in the parental origin-and hence the number of centrioles-between the 3PN IVF and the 3PN ICSI zygotes are likely to be the cause of the differences in karyotypes.
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Affiliation(s)
- Mette Warming Joergensen
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark. ; Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Johnny Hindkjaer
- The Fertility Clinic and Centre for Preimplantation Genetic diagnosis, Aarhus University Hospital, Skejby, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Steen Kolevraa
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Lone Sunde
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. ; Department of Clinical Genetics, Aarhus University Hospital, Skejby, Denmark
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Vagner J, Steiniche T, Stougaard M. In-situ hybridization-based quantification of hTR: a possible biomarker in malignant melanoma. Histopathology 2015; 66:747-51. [PMID: 25601620 DOI: 10.1111/his.12501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/10/2014] [Indexed: 12/20/2022]
Abstract
AIMS Telomerase is reactivated in most cancers and there is accumulating evidence that this is a driver event in malignant melanoma (MM). Thus, our aim was to evaluate if in-situ hybridization (ISH)-based quantification of telomerase RNA (hTR) could be used to distinguish MM from naevi, and if there was a correlation with the Breslow thickness. RESULTS AND METHODS We created a tissue microarray (TMA) from formalin-fixed and paraffin-embedded tissue samples from 17 MM and 23 naevi, performed ISH targeting hTR, and quantified the signals. We found a more than eightfold greater number of hTR signals per nucleus in the MM samples compared to the naevi, and a positive correlation (P = 0.0381) between the number of hTR signals per nucleus and the Breslow thickness. CONCLUSION Quantification of hTR ISH signals clearly distinguish MM from naevi (P < 0.0001) and the number of signals per nucleus correlates with the Breslow thickness, suggesting that hTR might be a valuable biomarker in MM. Furthermore, as ISH-based detection requires the presence of both hTR and telomerase reverse transcriptase (hTERT), it might be an indicator of active telomerase and thus have future relevance as a predictive biomarker for anti-telomerase treatment.
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Affiliation(s)
- Josephine Vagner
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, Building 18B, 8000, Aarhus C, Denmark
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41
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Abstract
Cellular heterogeneity has presented a significant challenge in the studies of biology. While most of our understanding is based on the analysis of ensemble average, individual cells may process information and respond to perturbations very differently. Presented here is a highly sensitive platform capable of measuring enzymatic activity at the single-cell level. The strategy innovatively combines a rolling circle-enhanced enzyme activity detection (REEAD) assay with droplet microfluidics. The single-molecule sensitivity of REEAD allows highly sensitive detection of enzymatic activities, i.e. at the single catalytic event level, whereas the microfluidics enables isolation of single cells. Further, confined reactions in picoliter-sized droplets significantly improve enzyme extraction from human cells or microorganisms and result in faster reaction kinetics. Taken together, the described protocol is expected to open up new possibilities in the single-cell research, particularly for the elucidation of heterogeneity in a population of cells.
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Affiliation(s)
- Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Mollers Alle 3, Building 1131, locale 328, 8000, Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Mollers Alle 3, Building 1131, locale 328, 8000, Aarhus C, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Mollers Alle 3, Building 1131, locale 328, 8000, Aarhus C, Denmark.
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Roy A, Tesauro C, Frøhlich R, Hede MS, Nielsen MJ, Kjeldsen E, Bonven B, Stougaard M, Gromova I, Knudsen BR. Decreased camptothecin sensitivity of the stem-cell-like fraction of Caco2 cells correlates with an altered phosphorylation pattern of topoisomerase I. PLoS One 2014; 9:e99628. [PMID: 24960044 PMCID: PMC4069021 DOI: 10.1371/journal.pone.0099628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 05/17/2014] [Indexed: 12/27/2022] Open
Abstract
The CD44+ and CD44− subpopulations of the colorectal cancer cell line Caco2 were analyzed separately for their sensitivities to the antitumor drug camptothecin. CD44+ cells were less sensitive to camptothecin than CD44− cells. The relative resistance of CD44+ cells was correlated with (i) reduced activity of the nuclear enzyme topoisomerase I and (ii) insensitivity of this enzyme to camptothecin when analyzed in extracts. In contrast, topoisomerase I activity was higher in extracts from CD44− cells and the enzyme was camptothecin sensitive. Topoisomerase I from the two subpopulations were differentially phosphorylated in a manner that appeared to determine the drug sensitivity and activity of the enzyme. This finding was further supported by the fact that phosphorylation of topoisomerase I in CD44+ cell extract by protein kinase CK2 converted the enzyme to a camptothecin sensitive, more active form mimicking topoisomerase I in extracts from CD44− cells. Conversely, dephosphorylation of topoisomerase I in extracts from CD44− cells rendered the enzyme less active and camptothecin resistant. These findings add to our understanding of chemotherapy resistance in the Caco2 CD44+ cancer stem cell model.
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Affiliation(s)
- Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria J. Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eigil Kjeldsen
- Hemodiagnostic Laboratory, Cancercytogenetic Section, Aarhus University Hospital, Aarhus, Denmark
| | - Bjarne Bonven
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Irina Gromova
- Genome Integrity Unit, Proteomics in Cancer, Danish Cancer Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- * E-mail:
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Proszek J, Roy A, Jakobsen AK, Frøhlich R, Knudsen BR, Stougaard M. Topoisomerase I as a biomarker: detection of activity at the single molecule level. Sensors (Basel) 2014; 14:1195-207. [PMID: 24434877 PMCID: PMC3926610 DOI: 10.3390/s140101195] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023]
Abstract
Human topoisomerase I (hTopI) is an essential cellular enzyme. The enzyme is often upregulated in cancer cells, and it is a target for chemotherapeutic drugs of the camptothecin (CPT) family. Response to CPT-based treatment is dependent on hTopI activity, and reduction in activity, and mutations in hTopI have been reported to result in CPT resistance. Therefore, hTOPI gene copy number, mRNA level, protein amount, and enzyme activity have been studied to explain differences in cellular response to CPT. We show that Rolling Circle Enhanced Enzyme Activity Detection (REEAD), allowing measurement of hTopI cleavage-religation activity at the single molecule level, may be used to detect posttranslational enzymatic differences influencing CPT response. These differences cannot be detected by analysis of hTopI gene copy number, mRNA amount, or protein amount, and only become apparent upon measuring the activity of hTopI in the presence of CPT. Furthermore, we detected differences in the activity of the repair enzyme tyrosyl-DNA phosphodiesterase 1, which is involved in repair of hTopI-induced DNA damage. Since increased TDP1 activity can reduce cellular CPT sensitivity we suggest that a combined measurement of TDP1 activity and hTopI activity in presence of CPT will be the best determinant for CPT response.
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Affiliation(s)
- Joanna Proszek
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark.
| | - Amit Roy
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark.
| | | | - Rikke Frøhlich
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark.
| | - Birgitta R Knudsen
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark.
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Abstract
Specific and sensitive detection of DNA-modifying enzymes represents a cornerstone in modern medical diagnostics. Many of the currently prevalent methods are not preferred in the clinics because they rely heavily on pre-amplification or post-separation steps. This editorial highlights the potential of adopting DNA-based nanosensors for the assessment of the activities of DNA-modifying enzymes, with emphasis on the topoisomerase and tyrosyl-DNA phosphodiesterase families. By underlining the existing challenges, we expect that the DNA-nanosensors may soon be promoted to clinical diagnostics via enzyme detection.
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Affiliation(s)
- Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000 Aarhus C, Denmark +45 7846 3672
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Juul S, Iacovelli F, Falconi M, Kragh SL, Christensen B, Frøhlich R, Franch O, Kristoffersen EL, Stougaard M, Leong KW, Ho YP, Sørensen ES, Birkedal V, Desideri A, Knudsen BR. Temperature-controlled encapsulation and release of an active enzyme in the cavity of a self-assembled DNA nanocage. ACS Nano 2013; 7:9724-9734. [PMID: 24168393 DOI: 10.1021/nn4030543] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University , Durham, North Carolina 27708, United States
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Tesauro C, Juul S, Arnò B, Nielsen CJF, Fiorani P, Frøhlich RF, Andersen FF, Desideri A, Stougaard M, Petersen E, Knudsen BR. Specific detection of topoisomerase I from the malaria causing P. falciparum parasite using isothermal rolling circle amplification. Annu Int Conf IEEE Eng Med Biol Soc 2013; 2012:2416-9. [PMID: 23366412 DOI: 10.1109/embc.2012.6346451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a Rolling-Circle-Enhance-Enzyme-Activity-Detection (REEAD) system with potential use for future point-of-care diagnosis of malaria. In the developed setup, specific detection of malaria parasites in crude blood samples is facilitated by the conversion of single Plasmodium falciparum topoisomerase I (pfTopI) mediated cleavage-ligation events, happening within nanometer dimensions, to micrometer-sized products readily detectable at the single molecule level in a fluorescence microscope. In principle, REEAD requires no special equipment and the readout is adaptable to simple colorimetric detection systems. Moreover, with regard to detection limit the presented setup is likely to outcompete standard gold immuno-based diagnostics. Hence, we believe the presented assay forms the basis for a new generation of easy-to-use diagnostic tools suitable for the malaria epidemic areas in developing countries.
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Affiliation(s)
- Cinzia Tesauro
- Department of Biology and Center of Biostatistics and Bioinformatics & NAST Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata, Rome, Italy
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Jensen PW, Falconi M, Kristoffersen EL, Simonsen AT, Cifuentes JB, Marcussen LB, Frøhlich R, Vagner J, Harmsen C, Juul S, Ho YP, Withers MA, Lupski JR, Koch J, Desideri A, Knudsen BR, Stougaard M. Real-time detection of TDP1 activity using a fluorophore-quencher coupled DNA-biosensor. Biosens Bioelectron 2013; 48:230-7. [PMID: 23693093 DOI: 10.1016/j.bios.2013.04.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/13/2013] [Indexed: 12/16/2022]
Abstract
Real-time detection of enzyme activities may present the easiest and most reliable way of obtaining quantitative analyses in biological samples. We present a new DNA-biosensor capable of detecting the activity of the potential anticancer drug target tyrosyl-DNA phosphodiesterase 1 (TDP1) in a very simple, high throughput, and real-time format. The biosensor is specific for Tdp1 even in complex biological samples, such as human cell extracts, and may consequently find future use in fundamental studies as well as a cancer predictive tool allowing fast analyses of diagnostic cell samples such as biopsies. TDP1 removes covalent 3'DNA adducts in DNA single-strand break repair. This enzymatic activity forms the basis of the design of the TDP1-biosensor, which consists of a short hairpin-forming oligonucleotide having a 5'fluorophore and a 3'quencher brought in close proximity by the secondary structure of the biosensor. The specific action of TDP1 removes the quencher, thereby enabling optical detection of the fluorophore. Since the enzymatic action of TDP1 is the only "signal amplification" the increase in fluorescence may easily be followed in real-time and allows quantitative analyses of TDP1 activity in pure enzyme fractions as well as in crude cell extracts. In the present study we demonstrate the specificity of the biosensor, its ability to quantitatively detect up- or down-regulated TDP1 activity, and that it may be used for measuring and for analyzing the mechanism of TDP1 inhibition.
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Affiliation(s)
- Pia W Jensen
- Department of Pathology, Aarhus University Hospital, Denmark
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Marcussen LB, Jepsen ML, Kristoffersen EL, Franch O, Proszek J, Ho YP, Stougaard M, Knudsen BR. DNA-based sensor for real-time measurement of the enzymatic activity of human topoisomerase I. Sensors (Basel) 2013; 13:4017-28. [PMID: 23529147 PMCID: PMC3673067 DOI: 10.3390/s130404017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/16/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Abstract
Sensors capable of quantitative real-time measurements may present the easiest and most accurate way to study enzyme activities. Here we present a novel DNA-based sensor for specific and quantitative real-time measurement of the enzymatic activity of the essential human enzyme, topoisomerase I. The basic design of the sensor relies on two DNA strands that hybridize to form a hairpin structure with a fluorophore-quencher pair. The quencher moiety is released from the sensor upon reaction with human topoisomerase I thus enabling real-time optical measurement of enzymatic activity. The sensor is specific for topoisomerase I even in raw cell extracts and presents a simple mean of following enzyme kinetics using standard laboratory equipment such as a qPCR machine or fluorimeter. Human topoisomerase I is a well-known target for the clinically used anti-cancer drugs of the camptothecin family. The cytotoxic effect of camptothecins correlates directly with the intracellular topoisomerase I activity. We therefore envision that the presented sensor may find use for the prediction of cellular drug response. Moreover, inhibition of topoisomerase I by camptothecin is readily detectable using the presented DNA sensor, suggesting a potential application of the sensor for first line screening for potential topoisomerase I targeting anti-cancer drugs.
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Affiliation(s)
- Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
| | - Morten Leth Jepsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Emil Laust Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Joanna Proszek
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (B.R.K.)
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (B.R.K.)
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Juul S, Nielsen CJF, Labouriau R, Roy A, Tesauro C, Jensen PW, Harmsen C, Kristoffersen EL, Chiu YL, Frøhlich R, Fiorani P, Cox-Singh J, Tordrup D, Koch J, Bienvenu AL, Desideri A, Picot S, Petersen E, Leong KW, Ho YP, Stougaard M, Knudsen BR. Droplet microfluidics platform for highly sensitive and quantitative detection of malaria-causing Plasmodium parasites based on enzyme activity measurement. ACS Nano 2012; 6:10676-83. [PMID: 23121492 PMCID: PMC3528816 DOI: 10.1021/nn3038594] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present an attractive new system for the specific and sensitive detection of the malaria-causing Plasmodium parasites. The system relies on isothermal conversion of single DNA cleavage-ligation events catalyzed specifically by the Plasmodium enzyme topoisomerase I to micrometer-sized products detectable at the single-molecule level. Combined with a droplet microfluidics lab-on-a-chip platform, this design allowed for sensitive, specific, and quantitative detection of all human-malaria-causing Plasmodium species in single drops of unprocessed blood with a detection limit of less than one parasite/μL. Moreover, the setup allowed for detection of Plasmodium parasites in noninvasive saliva samples from infected patients. During recent years malaria transmission has declined worldwide, and with this the number of patients with low-parasite density has increased. Consequently, the need for accurate detection of even a few parasites is becoming increasingly important for the continued combat against the disease. We believe that the presented droplet microfluidics platform, which has a high potential for adaptation to point-of-care setups suitable for low-resource settings, may contribute significantly to meet this demand. Moreover, potential future adaptation of the presented setup for the detection of other microorganisms may form the basis for the development of a more generic platform for diagnosis, fresh water or food quality control, or other purposes within applied or basic science.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | | | - Rodrigo Labouriau
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Cinzia Tesauro
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Pia W. Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Charlotte Harmsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Ya-Ling Chiu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Janet Cox-Singh
- School of Medicine, University of St Andrews, Fife KY16 9TF, Scotland and The Malaria Research Centre, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - David Tordrup
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jørn Koch
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Anne-Lise Bienvenu
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Alessandro Desideri
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Stephane Picot
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Eskild Petersen
- Department of Infectious Diseases, Institute of Clinical Medicine, Aarhus University Hospital-Skejby, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
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50
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Juul S, Ho YP, Stougaard M, Koch J, Andersen FF, Leong KW, Knudsen BR. Microfluidics-mediated isothermal detection of enzyme activity at the single molecule level. Annu Int Conf IEEE Eng Med Biol Soc 2012; 2011:3258-61. [PMID: 22255034 DOI: 10.1109/iembs.2011.6090885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Conventional analysis of enzymatic activity, often carried out on pools of cells, is blind to heterogeneity in the population. Here, we combine microfluidics with a previously developed isothermal rolling circle amplification-based assay to investigate multiple enzymatic activities in down to single cells. This microfluidics-meditated assay performs at very high sensitivity in picoliter incubators with small quantities of biological materials. Furthermore, we demonstrate the assay's capability of multiplexed detection of at least three enzyme activities at the single molecule level.
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Affiliation(s)
- Sissel Juul
- Department of Molecular Biology and Interdisciplinary Nanoscience Center, iNANO, Aarhus University, Denmark
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