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Douglas CM, Menon R, Montgomery J, Townsley R, Hilmi O, Buchanan MA, Robertson S, Petropoulakis L, Soraghan JJ, Lakany H, Mackenzie K. Vocal cord movement: can it be accurately graded? Ann R Coll Surg Engl 2024; 106:36-40. [PMID: 36263913 PMCID: PMC10757873 DOI: 10.1308/rcsann.2022.0091] [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] [Accepted: 06/19/2022] [Indexed: 06/16/2023] Open
Abstract
INTRODUCTION Flexible nasendoscopy (FNE) is the principal assessment method for vocal cord movement. Because the procedure is inherently subjective it may not be possible for clinicians to grade the degree of vocal cord movement reliably. The aim of this study was to assess the accuracy and consistency of grading vocal cord movement as viewed via FNE. METHODS Thirty FNE videos, without sound or clinical information, were assessed by six consultant head and neck surgeons. The surgeons were asked to assess and grade right and left vocal cord movement independently, based on a five-category scale. This process was repeated three times on separate occasions. Agreement and reliability were assessed. RESULTS Mean overall observed inter-rater agreement was 67.7% (sd 1.9) with the five-category scale, increasing to 91.4% (sd 1.9) when a three-category scale was derived. Mean overall observed intra-rater agreement was 78.3% (sd 9.7) for five categories, increasing to 93.1% (sd 3.3) for three categories. Discriminating vocal cord motion was less reliable using the five-category scale (k = 0.52) than with the three-category scale (k = 0.68). CONCLUSIONS This study demonstrates quantitatively that it is challenging to accurately and consistently grade subtle differences in vocal cord movement, as proven by the reduced agreement and reliability when using a five-point scale instead of a three-point scale. The study highlights the need for an objective measure to help in the assessment of vocal cord movement.
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Affiliation(s)
| | - R Menon
- University of Strathclyde, UK
| | | | | | - O Hilmi
- NHS Greater Glasgow and Clyde, UK
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Malchers F, Nogova L, van Attekum MH, Maas L, Brägelmann J, Bartenhagen C, Girard L, Bosco G, Dahmen I, Michels S, Weeden CE, Scheel AH, Meder L, Golfmann K, Schuldt P, Siemanowski J, Rehker J, Merkelbach-Bruse S, Menon R, Gautschi O, Heuckmann JM, Brambilla E, Asselin-Labat ML, Persigehl T, Minna JD, Walczak H, Ullrich RT, Fischer M, Reinhardt HC, Wolf J, Büttner R, Peifer M, George J, Thomas RK. Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer. J Clin Invest 2023; 133:e170217. [PMID: 37606995 PMCID: PMC10617767 DOI: 10.1172/jci170217] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
The discovery of frequent 8p11-p12 amplifications in squamous cell lung cancer (SQLC) has fueled hopes that FGFR1, located inside this amplicon, might be a therapeutic target. In a clinical trial, only 11% of patients with 8p11 amplification (detected by FISH) responded to FGFR kinase inhibitor treatment. To understand the mechanism of FGFR1 dependency, we performed deep genomic characterization of 52 SQLCs with 8p11-p12 amplification, including 10 tumors obtained from patients who had been treated with FGFR inhibitors. We discovered somatically altered variants of FGFR1 with deletion of exons 1-8 that resulted from intragenic tail-to-tail rearrangements. These ectodomain-deficient FGFR1 variants (ΔEC-FGFR1) were expressed in the affected tumors and were tumorigenic in both in vitro and in vivo models of lung cancer. Mechanistically, breakage-fusion-bridges were the source of 8p11-p12 amplification, resulting from frequent head-to-head and tail-to-tail rearrangements. Generally, tail-to-tail rearrangements within or in close proximity upstream of FGFR1 were associated with FGFR1 dependency. Thus, the genomic events shaping the architecture of the 8p11-p12 amplicon provide a mechanistic explanation for the emergence of FGFR1-driven SQLC. Specifically, we believe that FGFR1 ectodomain-deficient and FGFR1-centered amplifications caused by tail-to-tail rearrangements are a novel somatic genomic event that might be predictive of therapeutically relevant FGFR1 dependency.
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Affiliation(s)
- Florian Malchers
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lucia Nogova
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Martijn H.A. van Attekum
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lukas Maas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Mildred Scheel School of Oncology, Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
| | - Luc Girard
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Graziella Bosco
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Ilona Dahmen
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Sebastian Michels
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Clare E. Weeden
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andreas H. Scheel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Lydia Meder
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Kristina Golfmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Philipp Schuldt
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Janna Siemanowski
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Jan Rehker
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | | | - Oliver Gautschi
- University of Berne and Cantonal Hospital of Lucerne, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | | | | | - Marie-Liesse Asselin-Labat
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - John D. Minna
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Henning Walczak
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, United Kingdom
| | - Roland T. Ullrich
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jürgen Wolf
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Reinhard Büttner
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Martin Peifer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Julie George
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Department of Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Roman K. Thomas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Manjunath V, Thenral SG, Lakshmi BR, Nalini A, Bassi A, Karthikeyan KP, Piyusha K, Menon R, Malhotra A, Praveena LS, Anjanappa RM, Murugan SMS, Polavarapu K, Bardhan M, Preethish-Kumar V, Vengalil S, Nashi S, Sanga S, Acharya M, Raju R, Pai VR, Ramprasad VL, Gupta R. Large Region of Homozygous (ROH) Identified in Indian Patients with Autosomal Recessive Limb-Girdle Muscular Dystrophy with p.Thr182Pro Variant in SGCB Gene. Hum Mutat 2023. [DOI: 10.1155/2023/4362273] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The sarcoglycanopathies are autosomal recessive limb-girdle muscular dystrophies (LGMDs) caused by the mutations in genes encoding the α, β, γ, and δ proteins which stabilizes the sarcolemma of muscle cells. The clinical phenotype is characterized by progressive proximal muscle weakness with childhood onset. Muscle biopsy findings are diagnostic in confirming dystrophic changes and deficiency of one or more sarcoglycan proteins. In this study, we summarized 1,046 LGMD patients for which a precise diagnosis was identified using targeted sequencing. The most frequent phenotypes identified in the patients are LGMDR1 (19.7%), LGMDR4 (19.0%), LGMDR2 (17.5%), and MMD1 (14.5%). Among the reported genes, each of CAPN3, SGCB, and DYSF variants was reported in more than 10% of our study cohort. The most common variant SGCB p.Thr182Pro was identified in 146 (12.5%) of the LGMD patients, and in 97.9% of these patients, the variant was found to be homozygous. To understand the genetic structure of the patients carrying SGCB p.Thr182Pro, we genotyped 68 LGMD patients using a whole genome microarray. Analysis of the array data identified a large ~1 Mb region of homozygosity (ROH) (chr4:51817441-528499552) suggestive of a shared genomic region overlapping the recurrent missense variant and shared across all 68 patients. Haplotype analysis identified 133 marker haplotypes that were present in ~85.3% of the probands as a double allele and absent in all random controls. We also identified 5 markers (rs1910739, rs6852236, rs13122418, rs13353646, and rs6554360) which were present in a significantly higher proportion in the patients compared to random control set (
) and the population database. Of note, admixture analysis was suggestive of greater proportion of West Eurasian/European ancestry as compared to random controls. Haplotype analysis and frequency in the population database indicate a probable event of founder effect. Further systematic study is needed to identify the communities and regions where the SGCB p.Thr182Pro variant is observed in higher proportions. After identifying these communities and//or region, a screening program is needed to identify carriers and provide them counselling.
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ALAKWAA F, McCown P, Naik A, Schaub J, Menon R, Otto E, Nair V, Eddy S, Pyle L, Hartman J, Hodgin J, Nelson R, Brosius Division F, Kretzler M, Bjornstad P. WCN23-0471 THE ENHANCEMENT OF METALLOTHIONEIN BIND METAL PATHWAY WITH SGLT2 INHIBITORS IN KIDNEY PROXIMAL TUBULES OF ADOLESCENTS WITH TYPE 2 DIABETES USING SINGLE CELL RNA-SEQ DATA. Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.432] [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: 03/22/2023] Open
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Landi L, Tiseo M, Heukamp L, Menon R, de Marinis F, Minuti G, Cortinovis D, Delmonte A, Galetta D, Bertrand M, Zacher A, Gridelli C, Jacobs F, Chiari R, Verusio C, Giannarelli D, Crinò L, Cappuzzo F. P2.14-02 TP53 Mutations Affect Sensitivity to Lorlatinib in ROS1 Positive NSCLC: Final Results of the PFROST Trial. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.258] [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: 10/14/2022]
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Saikeerthi S, Menon R. A Psycho-Sociological Study on God men: What Draws Devotees of Various Socio-Economic Groups to Ashrams in India? CM 2022. [DOI: 10.18137/cardiometry.2022.23.350359] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
This paper observes the increasing influence of godmen in India and the socio-economic division among devotees that influences their decision to follow them. The study navigates through various social spheres and predominantly focuses on lower-income groups, middle-income groups, and upper-income groups to piece together the research paper. It focuses on in-depth interviews as a primary source of understanding these differences and is followed by possible deductions of the same, keeping in mind the hypothesis that there is a socio-economic divide in this seemingly secular framework of spirituality and religion, as defined by the devotees. These interviews are narrative analyzed to detect any recurring patterns within the economic groups and the following groups. Constructivism as a theory is used to understand how the arguments put forward by the interviewees are influenced by their social position in society and how they are inclined towards understanding reality on individual terms. The study’s findings prove that a possible correlation can be derived between an individual’s economic standing and expectations while following a certain godmen.
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Andrieu C, McNamee N, Larkin AM, Maguire A, Menon R, Mueller-Eisert J, Horgan N, Kennedy S, Gullo G, Crown J, Walsh N. Clinical Impact of Immune Checkpoint Inhibitor (ICI) Response, DNA Damage Repair (DDR) Gene Mutations and Immune-Cell Infiltration in Metastatic Melanoma Subtypes. Med Sci (Basel) 2022; 10:26. [PMID: 35736346 PMCID: PMC9230974 DOI: 10.3390/medsci10020026] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
Abstract
Molecular and histopathological analysis of melanoma subtypes has revealed distinct epidemiological, genetic, and clinical features. However, immunotherapy for advanced metastatic melanoma patients does not differ based on subtype. Response to immune checkpoint inhibitors (ICI) has been shown to vary, therefore, predictive biomarkers are needed in the design of precision treatments. Targeted sequencing and histopathological analysis (CD8 and CD20 immunohistochemistry) were performed on subtypes of metastatic melanoma (cutaneous melanoma (CM, n = 10); head and neck melanoma (HNM, n = 7); uveal melanoma (UM, n = 4); acral lentiginous melanoma (AM, n = 1) and mucosal melanoma (MM, n = 1) treated with ICI). Progression-free survival (PFS) was significantly associated with high CD8 expression (p = 0.025) and mutations in DNA damage repair (DDR) pathway genes (p = 0.012) in all subtypes but not with CD20 expression. Our study identified that immune cell infiltration and DDR gene mutations may have an impact in response to ICI treatment in metastatic melanoma but differs among subtypes. Therefore, a comprehensive understanding of the immune infiltration cells' role and DDR gene mutations in metastatic melanoma may identify prognostic biomarkers.
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Affiliation(s)
- Charlotte Andrieu
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Glasnevin, D09 E432 Dublin, Ireland; (C.A.); (N.M.); (A.-M.L.); (A.M.)
| | - Niamh McNamee
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Glasnevin, D09 E432 Dublin, Ireland; (C.A.); (N.M.); (A.-M.L.); (A.M.)
| | - Anne-Marie Larkin
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Glasnevin, D09 E432 Dublin, Ireland; (C.A.); (N.M.); (A.-M.L.); (A.M.)
- Department of Life Sciences, Institute of Technology Sligo, F91 YW50 Sligo, Ireland
| | - Alanna Maguire
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Glasnevin, D09 E432 Dublin, Ireland; (C.A.); (N.M.); (A.-M.L.); (A.M.)
| | - Roopika Menon
- Siemens Healthcare Diagnostics Products GmbH, 50667 Cologne, Germany; (R.M.); (J.M.-E.)
| | - Judith Mueller-Eisert
- Siemens Healthcare Diagnostics Products GmbH, 50667 Cologne, Germany; (R.M.); (J.M.-E.)
| | - Noel Horgan
- Royal Victoria Eye and Ear Hospital, Adelaide Road, D02 XK51 Dublin, Ireland; (N.H.); (S.K.)
| | - Susan Kennedy
- Royal Victoria Eye and Ear Hospital, Adelaide Road, D02 XK51 Dublin, Ireland; (N.H.); (S.K.)
| | - Giuseppe Gullo
- Department of Medical Oncology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland; (G.G.); (J.C.)
| | - John Crown
- Department of Medical Oncology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland; (G.G.); (J.C.)
| | - Naomi Walsh
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Glasnevin, D09 E432 Dublin, Ireland; (C.A.); (N.M.); (A.-M.L.); (A.M.)
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Heitz F, Lakis S, Harter P, Heikaus S, Sehouli J, Talwar J, Menon R, Ataseven B, Bertrand M, Schneider S, Mariotti E, Bommert M, Müller JN, Prader S, Leenders F, Hengsbach A, Gloeckner C, Braicu EI, Heukamp LC, du Bois A, Heuckmann JM. Cell-free tumor DNA, CA125 and HE4 for the objective assessment of tumor burden in patients with advanced high-grade serous ovarian cancer. PLoS One 2022; 17:e0262770. [PMID: 35130283 PMCID: PMC8820624 DOI: 10.1371/journal.pone.0262770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background The present prospective study aimed at determining the impact of cell-free tumor DNA (ct-DNA), CA125 and HE4 from blood and ascites for quantification of tumor burden in patients with advanced high-grade serous epithelial ovarian cancer (EOC). Methods Genomic DNA was extracted from tumor FFPE and ct-DNA from plasma before surgery and on subsequent post-surgical days. Extracted DNA was subjected to hybrid-capture based next generation sequencing. Blood and ascites were sampled before surgery and on subsequent post-surgical days. 20 patients (10 undergoing complete resection (TR0), 10 undergoing incomplete resection (TR>0)) were included. Results The minor allele frequency (MAF) of TP53 mutations in ct-DNA of all patients with TR0 decreased significantly, compared to only one patient with TR>0. It was not possible to distinguish between patients with TR0 and patients with TR>0, using CA125 and HE4 from blood and ascites. Conclusions Based upon the present findings, ct-DNA assessment in patients with high-grade serous EOC might help to better determine disease burden compared to standard tumor markers. Further studies should prospectively evaluate whether this enhancement of accuracy can help to optimize management of patients with EOC.
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Affiliation(s)
- Florian Heitz
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Corporate member of Freie Universität Berlin, Berlin, Germany
- Berlin Institute of Health, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
| | - Sotirios Lakis
- NEO New Oncology GmbH, Cologne, Germany
- ULTIVUE, Segrate Milan, Italy
| | - Philipp Harter
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | - Sebastian Heikaus
- Evangelische Kliniken Essen-Mitte, Center for Pathology, Essen, Germany
| | - Jalid Sehouli
- Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Corporate member of Freie Universität Berlin, Berlin, Germany
- Berlin Institute of Health, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Beyhan Ataseven
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Munich, Germany
| | - Miriam Bertrand
- NEO New Oncology GmbH, Cologne, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stephanie Schneider
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | - Mareike Bommert
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | - Sonia Prader
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department of Obstetrics and Gynecology, General Hospital (SABES-ASDAA), Brixen–Bres-sanone, Italy
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Inns-bruck, Austria
| | | | - Alexandra Hengsbach
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | | | | | - Andreas du Bois
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
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Devi A, Neogy S, Sharma S, Menon R, Tewari R. Characterization of argon ion irradiation induced changes in microstructure and mechanical property of binary Zr−2.9 wt% Sn alloy. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2021.109802] [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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Govindkumar B, Kavyashree B, Patel K, Sasidharan K, Siva Arumugam T, Thomas L, Praveena BKG, Raksha HN, Menon R, Acharya KK. Ex-Ex Primer: An experimentally validated tool for designing oligonucleotides spanning spliced nucleic acid regions from multiple species. J Biotechnol 2021; 343:1-6. [PMID: 34756973 DOI: 10.1016/j.jbiotec.2021.10.009] [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: 05/14/2021] [Revised: 08/09/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022]
Abstract
A comparative study of existing junction-primer-designing software revealed many limitations among them. Hence, we developed a new computational program, Ex-Ex Primer, which offers many improved, user-friendly features, and reliably creates junction primers and probes. This online suite can also be used to design primers/probes from other sites of nucleic acid recombination, insertion, deletion, or splicing, and regular probes/primers. The threshold for Tm difference between the complete junctional primer vs its partial sequence, which maps to one of the junctional regions, was changed based on an important observation made during the initial experimental validations. The tool is now thoroughly checked with RT-PCR and RT-qPCR experiments with more than 250 primer pairs over a few years. The junction-primer-designing features of the software are also better than other equivalent tools. Visualizing the exons and introns across transcripts, and enabling primer designing based on information from Ensembl, are some of the unique features of this tool. The primers suggested by the tool can be used to detect the expression of known transcripts, to test the existence of predicted DNA or RNA joints via hybridization-based techniques, or for validation and in silico analysis of RNA-Seq. URL: http://resource2.ibab.ac.in/exprimer/.
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Affiliation(s)
- Balagannavar Govindkumar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Basavaraju Kavyashree
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - Krishna Patel
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - Kalesh Sasidharan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - T Siva Arumugam
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - Lijo Thomas
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - B K G Praveena
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - H N Raksha
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - R Menon
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase 1, Bengaluru 560100, Karnataka, India
| | - K K Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Phase 1, Bengaluru 560100, Karnataka, India; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase 1, Bengaluru 560100, Karnataka, India.
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11
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Irving T, Menon R, Ciantar E. Trauma during pregnancy. BJA Educ 2021; 21:10-19. [PMID: 33456969 PMCID: PMC7808026 DOI: 10.1016/j.bjae.2020.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- T. Irving
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - R. Menon
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - E. Ciantar
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
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12
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Schatz S, Falk M, Jóri B, Ramdani HO, Schmidt S, Willing EM, Menon R, Groen HJM, Diehl L, Kröger M, Wesseler C, Griesinger F, Hoffknecht P, Tiemann M, Heukamp LC. Integration of Tumor Mutation Burden and PD-L1 Testing in Routine Laboratory Diagnostics in Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:cancers12061685. [PMID: 32599951 PMCID: PMC7353063 DOI: 10.3390/cancers12061685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, Non-small cell lung cancer (NSCLC) has evolved into a prime example for precision oncology with multiple FDA-approved “precision” drugs. For the majority of NSCLC lacking targetable genetic alterations, immune checkpoint inhibition (ICI) has become standard of care in first-line treatment or beyond. PD-L1 tumor expression represents the only approved predictive biomarker for PD-L1/PD-1 checkpoint inhibition by therapeutic antibodies. Since PD-L1-negative or low-expressing tumors may also respond to ICI, additional factors are likely to contribute in addition to PD-L1 expression. Tumor mutation burden (TMB) has emerged as a potential candidate; however, it is the most complex biomarker so far and might represent a challenge for routine diagnostics. We therefore established a hybrid capture (HC) next-generation sequencing (NGS) assay that covers all oncogenic driver alterations as well as TMB and validated TMB values by correlation with the assay (F1CDx) used for the CheckMate 227 study. Results of the first consecutive 417 patients analyzed in a routine clinical setting are presented. Data show that fast reliable comprehensive diagnostics including TMB and targetable alterations are obtained with a short turn-around time. Thus, even complex biomarkers can easily be implemented in routine practice to optimize treatment decisions for advanced NSCLC.
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Affiliation(s)
- Stefanie Schatz
- Institut für Hämatopathologie Hamburg, Fangdieckstraße 75A, 22547 Hamburg, Germany; (S.S.); (M.F.); (S.S.); (M.T.)
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
| | - Markus Falk
- Institut für Hämatopathologie Hamburg, Fangdieckstraße 75A, 22547 Hamburg, Germany; (S.S.); (M.F.); (S.S.); (M.T.)
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
| | - Balázs Jóri
- NEO New Oncology GmbH, Gottfried-Hagen-Straße 20, 51105 Cologne, Germany; (B.J.); (E.-M.W.); (R.M.)
| | - Hayat O. Ramdani
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
- Department of Hematology and Oncology, Pius-Hospital Oldenburg, Georgstraße 12, 26121 Oldenburg, Germany
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg Eppendorf, Martinistraße 52, 20246 Hamburg, Germany;
| | - Stefanie Schmidt
- Institut für Hämatopathologie Hamburg, Fangdieckstraße 75A, 22547 Hamburg, Germany; (S.S.); (M.F.); (S.S.); (M.T.)
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
| | - Eva-Maria Willing
- NEO New Oncology GmbH, Gottfried-Hagen-Straße 20, 51105 Cologne, Germany; (B.J.); (E.-M.W.); (R.M.)
| | - Roopika Menon
- NEO New Oncology GmbH, Gottfried-Hagen-Straße 20, 51105 Cologne, Germany; (B.J.); (E.-M.W.); (R.M.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Linda Diehl
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg Eppendorf, Martinistraße 52, 20246 Hamburg, Germany;
| | - Matthias Kröger
- Onkologische Schwerpunktpraxis, Kröger Ambulante Onkologie, Wiener Straße 1, 27568 Bremerhaven, Germany;
| | - Claas Wesseler
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
- Department of Internal Medicine and Pulmonology, Asklepios Klinikum Harburg, Eißendorfer Pferdeweg 52, 21075 Hamburg, Germany
| | - Frank Griesinger
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
- Department of Hematology and Oncology, Pius-Hospital Oldenburg, Georgstraße 12, 26121 Oldenburg, Germany
- Department of Internal Medicine-Oncology, University of Oldenburg, Georgstraße 12, 26121 Oldenburg, Germany
| | - Petra Hoffknecht
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
- Germany Department of Thorax Oncology, Niels-Stensen-Kliniken, Franziskus-Hospital Harderberg Alte Rothenfelder Straße 23, 49124 Georgsmarienhütte, Germany
| | - Markus Tiemann
- Institut für Hämatopathologie Hamburg, Fangdieckstraße 75A, 22547 Hamburg, Germany; (S.S.); (M.F.); (S.S.); (M.T.)
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
| | - Lukas C. Heukamp
- Institut für Hämatopathologie Hamburg, Fangdieckstraße 75A, 22547 Hamburg, Germany; (S.S.); (M.F.); (S.S.); (M.T.)
- Lung Cancer Network NOWEL, 26129 Oldenburg, Germany; (H.O.R.); (C.W.); (F.G.); (P.H.)
- Correspondence: or ; Tel.: +49-176-200-56495
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13
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Lamont RF, Richardson LS, Boniface JJ, Cobo T, Exner MM, Christensen IB, Forslund SK, Gaba A, Helmer H, Jørgensen JS, Khan RN, McElrath TF, Petro K, Rasmussen M, Singh R, Tribe RM, Vink JS, Vinter CA, Zhong N, Menon R. Commentary on a combined approach to the problem of developing biomarkers for the prediction of spontaneous preterm labor that leads to preterm birth. Placenta 2020; 98:13-23. [PMID: 33039027 DOI: 10.1016/j.placenta.2020.05.007] [Citation(s) in RCA: 16] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Globally, preterm birth has replaced congenital malformation as the major cause of perinatal mortality and morbidity. The reduced rate of congenital malformation was not achieved through a single biophysical or biochemical marker at a specific gestational age, but rather through a combination of clinical, biophysical and biochemical markers at different gestational ages. Since the aetiology of spontaneous preterm birth is also multifactorial, it is unlikely that a single biomarker test, at a specific gestational age will emerge as the definitive predictive test. METHODS The Biomarkers Group of PREBIC, comprising clinicians, basic scientists and other experts in the field, with a particular interest in preterm birth have produced this commentary with short, medium and long-term aims: i) to alert clinicians to the advances that are being made in the prediction of spontaneous preterm birth; ii) to encourage clinicians and scientists to continue their efforts in this field, and not to be disheartened or nihilistic because of a perceived lack of progress and iii) to enable development of novel interventions that can reduce the mortality and morbidity associated with preterm birth. RESULTS Using language that we hope is clear to practising clinicians, we have identified 11 Sections in which there exists the potential, feasibility and capability of technologies for candidate biomarkers in the prediction of spontaneous preterm birth and how current limitations to this research might be circumvented. DISCUSSION The combination of biophysical, biochemical, immunological, microbiological, fetal cell, exosomal, or cell free RNA at different gestational ages, integrated as part of a multivariable predictor model may be necessary to advance our attempts to predict sPTL and PTB. This will require systems biological data using "omics" data and artificial intelligence/machine learning to manage the data appropriately. The ultimate goal is to reduce the mortality and morbidity associated with preterm birth.
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Affiliation(s)
- R F Lamont
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Division of Surgery, Northwick Park Institute for Medical Research Campus, University College London, London, UK.
| | - L S Richardson
- Dept of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Dept. Electrical and Computer Engineering Texas A&M University, College Station, TX, USA
| | - J J Boniface
- Sera Prognostics, Inc., 2749 East Parleys Way, Suite 200, Salt Lake City, UT, 84109, USA
| | - T Cobo
- BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecología, Obstetrícia I Neonatología, Fetal i+D Fetal Medicine Research Center, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona. Barcelona. Spain, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - M M Exner
- Hologic, Inc., 10210 Genetic Center Dr, San Diego, CA, 92121, USA
| | | | - S K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
| | - A Gaba
- Department of Obstetrics and Maternal-fetal Medicine, Vienna Medical University, Austria
| | - H Helmer
- Department of Obstetrics and Maternal-fetal Medicine, Vienna Medical University, Austria
| | - J S Jørgensen
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre for Innovative Medical Technologies (CIMT), Odense University Hospital, Kløvervænget 8, 5000, Odense C, Denmark; Odense Patient Data Explorative Network (OPEN), Odense University Hospital/University of Southern Denmark, J. B. Winsløws Vej 9 a, 3. Floor, 5000, Odense C, Denmark
| | - R N Khan
- Division of Medical Science and Graduate Entry Medicine, School of Medicine, University of Nottingham, Room 4115, Medical School, Royal Derby Hospital Centre, Derby, DE22 3DT, UK
| | | | - K Petro
- Hologic, Inc., 10210 Genetic Center Dr, San Diego, CA, 92121, USA
| | - M Rasmussen
- MIRVIE Inc., 820 Dubuque Ave., South San Francisco, CA, 94080, USA
| | - R Singh
- ARCEDI Biotech ApS, Aarhus, Denmark
| | - R M Tribe
- Dept. of Women and Children's Health, School of Life Course Sciences, King's College London, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - J S Vink
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - C A Vinter
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - N Zhong
- New York State Institute for Basic Research in Developmental Disabilities, 105 Forest Hill Road, Staten Island, NY, 10314, USA
| | - R Menon
- Dept of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Dept. Electrical and Computer Engineering Texas A&M University, College Station, TX, USA.
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14
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Jivraj BA, Ahmed N, Karia K, Menon R, Robertson E, Sodha A, Wormald JCR, O'hara J, Jeelani O, Dunaway D, James G, Ong J. A 24-month cost and outcome analysis comparing traditional fronto-orbital advancment and remodeling with endoscopic strip craniectomy and molding helmet in the management of unicoronal craniosynostosis: A retrospective bi-institutional review. JPRAS Open 2020; 20:35-42. [PMID: 32158870 PMCID: PMC7061657 DOI: 10.1016/j.jpra.2019.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 11/12/2022] Open
Abstract
Introduction Endoscopic strip craniectomy with helmeting (ESCH) has been shown to be a safe and efficacious alternative to fronto-orbital remodeling (FOR) for selected children with craniosynostosis. In addition to clinical factors, there may be economic benefits from the use of ESCH instead of FOR. Methods A retrospective review of 23 patients with nonsyndromic unicoronal craniosynostosis (UCS) treated with FOR was carried out at Great Ormond Street Hospital (GOSH) for Children in London, UK. Secondary data were used for the ESCH cohort from a paper published by Jimenez and Barone (2013). Data were collected on surgical time, transfusion rates, length of hospital stay, adverse event rates, reintervention rates, and overall costs. Costs were categorized and then assigned to the appropriate data sets. Results The mean age of patients undergoing FOR (vs. ESCH) was 17.4 mo (vs. 3.1 mo) with a mean surgical time of 234 min (vs. 55 min), mean transfusion volume of 221.6 mL (vs. 80.0 mL), mean transfusion rate of 14/23 (vs. 2/115), and a total immediate overnight stay of 3.13 days (vs. 97% next-day discharge). The FOR group had a higher adverse event rate (5/23 vs. 4/115, p=<0.005) and a higher number requiring extraocular muscle surgery (4/23 vs. 7/109, p=0.16). There was a substantial difference in overall costs between the two groups. Total variance cost for the FOR group was £7436.5 vs. £4951.35, representing a cost difference of £2485.15 over the 24-month study period. Conclusion ESCH, in comparison to FOR, appears as a more economical method in the management of USC patients, as well as having clinical benefits including reduced adverse event rate and improved ophthalmic outcomes.
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Affiliation(s)
- B A Jivraj
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - N Ahmed
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - K Karia
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - R Menon
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - E Robertson
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - A Sodha
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - J C R Wormald
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - J O'hara
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - O Jeelani
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - D Dunaway
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - G James
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
| | - J Ong
- Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, UK
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15
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Ponangi U, Kapadia A, Menon R. 778 A Novel Approach to Prevent No-Reflow in Acute Myocardial Infarction Patients With Large Thrombus Burden. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Gautschi O, Menon R, Bertrand M, Murer C, Diebold J. Capmatinib and Osimertinib Combination Therapy for EGFR-Mutant Lung Adenocarcinoma. J Thorac Oncol 2020; 15:e13-e15. [DOI: 10.1016/j.jtho.2019.07.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 10/25/2022]
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17
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Landi L, Tiseo M, Heukamp L, Menon R, Spitaleri G, Cortinovis D, Delmonte A, Galetta D, D’Arcangelo M, D’Incà F, Bertrand M, Jóri B, Zacher A, Gridelli C, Novello S, Chiari R, Verusio C, Crinò L, Cappuzzo F. Secondary ROS1 mutations and lorlatinib sensitivity in crizotinib-refractory ROS1 positive NSCLC: Results of the prospective PFROST trial. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz260.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Nanda S, Menon R, Kumari S, Mohan N, Kesavadas C. Visual-verbal paired associate memory in mild cognitive impairment: A neuropsychological and brain volumetric study. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.791] [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: 10/25/2022]
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19
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Scott KP, Grimaldi R, Cunningham M, Sarbini SR, Wijeyesekera A, Tang MLK, Lee JCY, Yau YF, Ansell J, Theis S, Yang K, Menon R, Arfsten J, Manurung S, Gourineni V, Gibson GR. Developments in understanding and applying prebiotics in research and practice-an ISAPP conference paper. J Appl Microbiol 2019; 128:934-949. [PMID: 31446668 DOI: 10.1111/jam.14424] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022]
Abstract
AIMS The concept of using specific dietary components to selectively modulate the gut microbiota to confer a health benefit, defined as prebiotics, originated in 1995. In 2018, a group of scientists met at the International Scientific Association for Probiotics and Prebiotics annual meeting in Singapore to discuss advances in the prebiotic field, focussing on issues affecting functionality, research methodology and geographical differences. METHODS AND RESULTS The discussion ranged from examining scientific literature supporting the efficacy of established prebiotics, to the prospects for establishing health benefits associated with novel compounds, isolated from different sources. CONCLUSIONS While many promising candidate prebiotics from across the globe have been highlighted in preliminary research, there are a limited number with both demonstrated mechanism of action and defined health benefits as required to meet the prebiotic definition. Prebiotics are part of a food industry with increasing market sales, yet there are great disparities in regulations in different countries. Identification and commercialization of new prebiotics with unique health benefits means that regulation must improve and remain up-to-date so as not to risk stifling research with potential health benefits for humans and other animals. SIGNIFICANCE AND IMPACT OF STUDY This summary of the workshop discussions indicates potential avenues for expanding the range of prebiotic substrates, delivery methods to enhance health benefits for the end consumer and guidance to better elucidate their activities in human studies.
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Affiliation(s)
- K P Scott
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - R Grimaldi
- Food and Nutritional Sciences, University of Reading, Reading, UK
| | - M Cunningham
- Metagenics (Aust) Pty Ltd., Virginia, Queensland, Australia
| | - S R Sarbini
- Department of Crop Science, Universiti Putra Malaysia, Bintulu Campus, Malaysia
| | - A Wijeyesekera
- Food and Nutritional Sciences, University of Reading, Reading, UK
| | - M L K Tang
- Department of Allergy and Immunology, The Royal Children's Hospital, Parkville, Melbourne, VIC, Australia
| | - J C-Y Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Y F Yau
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - J Ansell
- Zespri International Ltd, Mt Maunganui, New Zealand
| | - S Theis
- Beneo-Institute, Obrigheim, Germany
| | - K Yang
- Departments of Obstetrics and Gynaecology and Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - R Menon
- The Bell Institute of Health and Nutrition, General Mills Inc., Minneapolis, MN, USA
| | - J Arfsten
- Nestlé Product and Technology Center Dairy, Konolfingen, Switzerland
| | - S Manurung
- Reckitt Benckiser, Nijmegen, The Netherlands
| | - V Gourineni
- Ingredion Incorporated, Bridgewater, NJ, USA
| | - G R Gibson
- Food and Nutritional Sciences, University of Reading, Reading, UK
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20
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Michels S, Massutí B, Schildhaus HU, Franklin J, Sebastian M, Felip E, Grohé C, Rodriguez-Abreu D, Abdulla DS, Bischoff H, Brandts C, Carcereny E, Corral J, Dingemans AMC, Pereira E, Fassunke J, Fischer RN, Gardizi M, Heukamp L, Insa A, Kron A, Menon R, Persigehl T, Reck M, Riedel R, Rothschild SI, Scheel AH, Scheffler M, Schmalz P, Smit EF, Limburg M, Provencio M, Karachaliou N, Merkelbach-Bruse S, Hellmich M, Nogova L, Büttner R, Rosell R, Wolf J. Safety and Efficacy of Crizotinib in Patients With Advanced or Metastatic ROS1-Rearranged Lung Cancer (EUCROSS): A European Phase II Clinical Trial. J Thorac Oncol 2019; 14:1266-1276. [DOI: 10.1016/j.jtho.2019.03.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
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21
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Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 2019; 362:1165-1170. [PMID: 30523111 DOI: 10.1126/science.aat6768] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/26/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance-negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.
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Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andrea Roderwieser
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Esther Walter
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Judith Gecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Laura Kerschke
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | | | | | - Moritz Gartlgruber
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Sabine Hartlieb
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bram de Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frederik Sand
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Fakhera Ikram
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janina Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Wenzel Vogel
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Barbara Krug
- Department of Diagnostic and Interventional Radiology, University Hospital of Cologne, Cologne, Germany
| | - Matthias Schmidt
- Department of Nuclear Medicine, University of Cologne, Cologne, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Computer Science, TU Dortmund, Dortmund, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, Cologne, Germany.,Department of Informatics, University of Cologne, Cologne, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Department of Pediatric Pathology, University of Kiel, Kiel, Germany
| | - Monika Ortmann
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute (UPCI), Hillman Cancer Center, Pittsburgh, PA, USA
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Medical Oncology, West German Cancer Center Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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22
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Lozovyy V, Richardson L, Saade G, Menon R. 1027: Screening for membrane progesterone receptors: labor associated functional progesterone withdrawal in fetal membranes. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2018.11.1051] [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: 11/29/2022]
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23
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Schatz S, Falk M, Menon R, Heukamp L, Roeper J, Griesinger F, Tiemann M. Hybrid capture NGS reliably detects a spectrum of clinically significant genetic aberrations in both, primary diagnostics and the relapse scenario. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy292.054] [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: 11/12/2022] Open
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24
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Hengsbach A, Lakis S, Heitz F, Talwar A, Sehouli J, Bommert M, Bertrand M, Ataseven B, Müller JN, Schneider S, Mariotti E, Prader S, Menon R, Leenders F, Heukamp LC, Braicu I, Glöckner C, du Bois A, Heuckmann JM. Liquid biopsy zur objektiven Beurteilung des post-operativen Tumorrestes bei Patientinnen mit fortgeschrittenem high-grade serösem Ovarialkarzinom. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- A Hengsbach
- Kliniken Essen-Mitte (KEM), Gynäkologische Onkologie, Essen, Deutschland
| | - S Lakis
- NEO New Oncology, Köln, Deutschland
| | - F Heitz
- Kliniken Essen-Mitte (KEM), Essen, Deutschland
| | - A Talwar
- NEO New Oncology, Köln, Deutschland
| | - J Sehouli
- Charité – Universitätsmedizin Berlin, Berlin, Deutschland
| | - M Bommert
- Kliniken Essen Mitte, Gynäkologie und Gynäkologische Onkologie, Essen, Deutschland
| | | | - B Ataseven
- Kliniken Essen Mitte, Essen, Deutschland
| | | | - S Schneider
- Kliniken Essen Mitte, Gynäkologie und Gynäkologische Onkologie, Essen, Deutschland
| | | | - S Prader
- Kliniken Essen Mitte, Essen, Deutschland
| | - R Menon
- NEO New Oncology, Köln, Deutschland
| | | | | | - I Braicu
- Charité – Universitätsmedizin Berlin, Berlin, Deutschland
| | | | - A du Bois
- Kliniken Essen Mitte, Essen, Deutschland
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25
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Menon R, Kumar V, Laskhman I, Nair R. Hemispheric infarct following a cerebellar hematoma: A rare coincidence. Asian J Neurosurg 2018; 13:449-452. [PMID: 29682058 PMCID: PMC5898129 DOI: 10.4103/ajns.ajns_227_16] [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] [Indexed: 11/05/2022] Open
Abstract
Concomitant cerebral infarction developing soon after a parenchymal intracerebral hemorrhage is a rare occurrence. Usually, these remote site changes follow tumor decompression and are associated with hemorrhagic changes rather than infarcts. We report a case of a fatal malignant internal carotid territory infarct in a hospitalized patient being conservatively managed for a vermian hematoma and discuss the probable pathophysiology. Stroke physicians need to be aware that spontaneous intracerebral hematoma patients have a potential threat of developing large vessel occlusion with malignant cerebral infarcts, especially after surgical decompression. Although the exact pathogenesis is unknown, size of the clot, intraventricular hemorrhage, hydrocephalus, and aggressive reduction of blood pressure appear to be predictive factors.
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Affiliation(s)
- R Menon
- Department of Neurosurgery, Kasturba Medical College, Manipal University, Manipal, Karnataka
| | - Vinod Kumar
- Department of Neurosurgery, Kasturba Medical College, Manipal University, Manipal, Karnataka
| | - I Laskhman
- Department of Neurosurgery, Kasturba Medical College, Manipal University, Manipal, Karnataka
| | - Rajesh Nair
- Department of Neurosurgery, Kasturba Medical College, Manipal University, Manipal, Karnataka
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26
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Abstract
Sarcoma-180 tumour (S-180) exhibits natural resistance to bouvardin (NSC 259968), a protein synthesis inhibitor that also inhibits RNA and DNA synthesis when administered over a range of non-toxic doses using 0.9 % NaCl as a vehicle. However, using Tween-80 as a vehicle, there is a substantial enhancement of cytotoxicity and a subsequent increase in the life span of animals bearing the S-180 tumour. This observation was substantiated in vitro by exposing S-180 cells to 10−6 M bouvardin in the presence and absence of Tween-80. Bouvardin, 10−6 M, in the absence of Tween-80, inhibited the incorporation of [3H]uridine by 46 %, whereas the presence of Tween-80 resulted in a 66 % inhibition of uridine incorporation.
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27
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Chitnis M, Menon R, Adwankar M, Satyamoorthy K. Inhibition of Macromolecular Synthesis in P388 Mouse Leukemia Ascites Cells by Bouvardin (NSC 259968). Tumori 2018; 71:261-6. [PMID: 4024280 DOI: 10.1177/030089168507100307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bouvardin, a new antineoplastic plant product, inhibits macromolecular synthesis in P388 cells in a dose-dependent manner. At the same concentration of bouvardin, protein synthesis was inhibited to a greater extent than the synthesis of DNA and RNA. There was a reversal of inhibition of both DNA and RNA synthesis after the cells were washed free of bouvardin. However, there was partial reversal of inhibition of protein synthesis when the cells were washed free of the drug.
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Affiliation(s)
- R Menon
- Paediatric Department, Clarendon, Leeds
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29
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Drapkin BJ, George J, Christensen CL, Mino-Kenudson M, Dries R, Sundaresan T, Phat S, Myers DT, Zhong J, Igo P, Hazar-Rethinam MH, Licausi JA, Gomez-Caraballo M, Kem M, Jani KN, Azimi R, Abedpour N, Menon R, Lakis S, Heist RS, Büttner R, Haas S, Sequist LV, Shaw AT, Wong KK, Hata AN, Toner M, Maheswaran S, Haber DA, Peifer M, Dyson N, Thomas RK, Farago AF. Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts. Cancer Discov 2018; 8:600-615. [PMID: 29483136 DOI: 10.1158/2159-8290.cd-17-0935] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/12/2018] [Accepted: 02/21/2018] [Indexed: 11/16/2022]
Abstract
Small cell lung cancer (SCLC) patient-derived xenografts (PDX) can be generated from biopsies or circulating tumor cells (CTC), though scarcity of tissue and low efficiency of tumor growth have previously limited these approaches. Applying an established clinical-translational pipeline for tissue collection and an automated microfluidic platform for CTC enrichment, we generated 17 biopsy-derived PDXs and 17 CTC-derived PDXs in a 2-year timeframe, at 89% and 38% efficiency, respectively. Whole-exome sequencing showed that somatic alterations are stably maintained between patient tumors and PDXs. Early-passage PDXs maintain the genomic and transcriptional profiles of the founder PDX. In vivo treatment with etoposide and platinum (EP) in 30 PDX models demonstrated greater sensitivity in PDXs from EP-naïve patients, and resistance to EP corresponded to increased expression of a MYC gene signature. Finally, serial CTC-derived PDXs generated from an individual patient at multiple time points accurately recapitulated the evolving drug sensitivities of that patient's disease. Collectively, this work highlights the translational potential of this strategy.Significance: Effective translational research utilizing SCLC PDX models requires both efficient generation of models from patients and fidelity of those models in representing patient tumor characteristics. We present approaches for efficient generation of PDXs from both biopsies and CTCs, and demonstrate that these models capture the mutational landscape and functional features of the donor tumors. Cancer Discov; 8(5); 600-15. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
| | - Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | | | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ruben Dries
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tilak Sundaresan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sarah Phat
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - David T Myers
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Peter Igo
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | - Joseph A Licausi
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Marina Kem
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Roxana Azimi
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Nima Abedpour
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | | | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Reinhard Büttner
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - Stefan Haas
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Kwok-Kin Wong
- Department of Hematology and Oncology, New York University Langone Medical School, New York, New York
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Mehmet Toner
- Harvard Medical School, Boston, Massachusetts.,Center for Engineering in Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts.,Shriners Hospital for Children, Boston, Massachusetts
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany. .,Department of Pathology, University Hospital Cologne, Cologne, Germany.,German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anna F Farago
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
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30
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Plenker D, Bertrand M, de Langen AJ, Riedel R, Lorenz C, Scheel AH, Müller J, Brägelmann J, Daßler-Plenker J, Kobe C, Persigehl T, Kluge A, Wurdinger T, Schellen P, Hartmann G, Zacherle T, Menon R, Thunnissen E, Büttner R, Griesinger F, Wolf J, Heukamp L, Sos ML, Heuckmann JM. Structural Alterations of MET Trigger Response to MET Kinase Inhibition in Lung Adenocarcinoma Patients. Clin Cancer Res 2017; 24:1337-1343. [PMID: 29284707 DOI: 10.1158/1078-0432.ccr-17-3001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Dennis Plenker
- Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany.,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | | | - Adrianus J de Langen
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, the Netherlands
| | - Richard Riedel
- Department of Internal Medicine, Center for Integrated Oncology Köln Bonn, University Hospital Cologne, Cologne, Germany
| | - Carina Lorenz
- Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany.,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Andreas H Scheel
- Institute of Pathology, Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | | | - Johannes Brägelmann
- Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany.,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Juliane Daßler-Plenker
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Carsten Kobe
- Department of Nuclear Medicine, University Hospital of Cologne, Cologne, Germany
| | - Thorsten Persigehl
- Department of Radiology, University Hospital of Cologne, Cologne, Germany
| | - Alexander Kluge
- Institute for Diagnostic and Interventional Radiology, Pius-Hospital, Medical Campus University of Oldenburg, Oldenburg, Germany
| | - Thomas Wurdinger
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands.,Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands.,Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, Charlestown, Massachusetts
| | - Pepijn Schellen
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands.,Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Gunther Hartmann
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | | | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Reinhard Büttner
- Institute of Pathology, Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Frank Griesinger
- Lung Cancer Network NOWEL, Oldenburg, Germany.,Department of Hematology and Oncology, Pius-Hospital, University Department Internal Medicine-Oncology, Medical Campus University of Oldenburg, Oldenburg, Germany
| | - Jürgen Wolf
- Department of Internal Medicine, Center for Integrated Oncology Köln Bonn, University Hospital Cologne, Cologne, Germany
| | - Lukas Heukamp
- NEO New Oncology GmbH, Köln, Germany.,Lung Cancer Network NOWEL, Oldenburg, Germany.,Institute for Hematopathology, Hamburg, Germany
| | - Martin L Sos
- Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany. .,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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31
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Nanda S, Menon R, Kesavadas C, Kumari S. A pilot study on mapping structural and functional connectivity in early Alzheimer's disease(AD) in comparison to stable mild cognitive impairment (MCI) and healthy controls. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.2164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Müller JN, Falk M, Talwar J, Neemann N, Mariotti E, Bertrand M, Zacherle T, Lakis S, Menon R, Gloeckner C, Tiemann M, Heukamp LC, Thomas RK, Griesinger F, Heuckmann JM. Concordance between Comprehensive Cancer Genome Profiling in Plasma and Tumor Specimens. J Thorac Oncol 2017; 12:1503-1511. [DOI: 10.1016/j.jtho.2017.07.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/08/2017] [Accepted: 07/03/2017] [Indexed: 12/30/2022]
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Hu ASY, Menon R, Gunnarsson R, de Costa A. Risk factors for conversion of laparoscopic cholecystectomy to open surgery - A systematic literature review of 30 studies. Am J Surg 2017; 214:920-930. [PMID: 28739121 DOI: 10.1016/j.amjsurg.2017.07.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 12/12/2016] [Revised: 07/10/2017] [Accepted: 07/16/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND The study aims to evaluate the methodological quality of publications relating to predicting the need of conversion from laparoscopic to open cholecystectomy and to describe identified prognostic factors. METHOD Only English full-text articles with their own unique observations from more than 300 patients were included. Only data using multivariate analysis of risk factors were selected. Quality assessment criteria stratifying the risk of bias were constructed and applied. RESULTS The methodological quality of the studies were mostly heterogeneous. Most studies performed well in half of the quality criteria and considered similar risk factors, such as male gender and old age, as significant. Several studies developed prediction models for risk of conversion. Independent risk factors appeared to have additive effects. CONCLUSION A detailed critical review of studies of prediction models and risk stratification for conversion from laparoscopic to open cholecystectomy is presented. One study is identified of high quality with a potential to be used in clinical practice, and external validation of this model is recommended.
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Affiliation(s)
- Alan Shiun Yew Hu
- Cairns Clinical School, College of Medicine and Dentistry, James Cook University, QLD, 4870, Australia.
| | - R Menon
- Cairns Clinical School, College of Medicine and Dentistry, James Cook University, QLD, 4870, Australia.
| | - R Gunnarsson
- Cairns Clinical School, College of Medicine and Dentistry, James Cook University, QLD, 4870, Australia; Research and Development Unit, Primary Health Care and Dental Care, Narhalsan, Southern Älvsborg County, Region Västra Götaland, Sweden; Department of Public Health and Community Medicine, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Sweden.
| | - A de Costa
- Cairns Clinical School, College of Medicine and Dentistry, James Cook University, QLD, 4870, Australia.
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34
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Malchers F, Ercanoglu M, Schütte D, Castiglione R, Tischler V, Michels S, Dahmen I, Brägelmann J, Menon R, Heuckmann JM, George J, Ansén S, Sos ML, Soltermann A, Peifer M, Wolf J, Büttner R, Thomas RK. Mechanisms of Primary Drug Resistance in FGFR1-Amplified Lung Cancer. Clin Cancer Res 2017. [PMID: 28630215 DOI: 10.1158/1078-0432.ccr-17-0478] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purpose: The 8p12-p11 locus is frequently amplified in squamous cell lung cancer (SQLC); the receptor tyrosine kinase fibroblast growth factor receptor 1 (FGFR1) being one of the most prominent targets of this amplification. Thus, small molecules inhibiting FGFRs have been employed to treat FGFR1-amplified SQLC. However, only about 11% of such FGFR1-amplified tumors respond to single-agent FGFR inhibition and several tumors exhibited insufficient tumor shrinkage, compatible with the existence of drug-resistant tumor cells.Experimental Design: To investigate possible mechanisms of resistance to FGFR inhibition, we studied the lung cancer cell lines DMS114 and H1581. Both cell lines are highly sensitive to three different FGFR inhibitors, but exhibit sustained residual cellular viability under treatment, indicating a subpopulation of existing drug-resistant cells. We isolated these subpopulations by treating the cells with constant high doses of FGFR inhibitors.Results: The FGFR inhibitor-resistant cells were cross-resistant and characterized by sustained MAPK pathway activation. In drug-resistant H1581 cells, we identified NRAS amplification and DUSP6 deletion, leading to MAPK pathway reactivation. Furthermore, we detected subclonal NRAS amplifications in 3 of 20 (15%) primary human FGFR1-amplified SQLC specimens. In contrast, drug-resistant DMS114 cells exhibited transcriptional upregulation of MET that drove MAPK pathway reactivation. As a consequence, we demonstrate that rational combination therapies resensitize resistant cells to treatment with FGFR inhibitors.Conclusions: We provide evidence for the existence of diverse mechanisms of primary drug resistance in FGFR1-amplified lung cancer and provide a rational strategy to improve FGFR inhibitor therapies by combination treatment. Clin Cancer Res; 23(18); 5527-36. ©2017 AACR.
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Affiliation(s)
- Florian Malchers
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Meryem Ercanoglu
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Daniel Schütte
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | | | - Verena Tischler
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Sebastian Michels
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Johannes Brägelmann
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany
| | | | | | - Julie George
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Sascha Ansén
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Martin L Sos
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Molecular Pathology, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Alex Soltermann
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Martin Peifer
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jürgen Wolf
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | | | - Roman K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany. .,Institute of Pathology, University of Cologne, Cologne, Germany.,German Cancer Research Center (DKFZ), Heidelberg, German Cancer Consortium (DKTK), Partner site Heidelberg, Germany
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Heitz F, Lakis S, Harter P, Sehouli J, Talwar J, Sprokmann M, Bertrand M, Ataseven B, Mariotti E, Schneider S, Müller JN, Menon R, Prader S, Leenders F, Hengsbach A, Gloeckner C, Braicu EI, Heukamp LC, Heuckmann J, Du Bois A. Cell-free tumor DNA in peri-operative blood samples from advanced high-grade serous ovarian cancer patients with and without complete resection. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.5555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5555 Background: Surgical outcome is an important prognostic factor in advanced high-grade serous ovarian cancer (HGOC). Intra-operative determination of residual disease may be prone to subjective bias. Methods: We prospectively collected and analyzed tumor tissue and plasma from 21 pts with FIGO IIIC-IV HGOC. All tumor specimen showed loss of TP53 in immunohistochemistry. Tumor DNA from tissue and peri-operative cell-free DNA at baseline (BL) and at d(ays) 1, d4 and d10 were subjected to comprehensive hybrid-capture based next-generation sequencing (NEO New Oncology GmbH, Cologne, Germany). Results: The initial cohort comprised 10 pts without (TR>0) and 11 pts with complete resection TR0, with a total of 43 somatic genomic alterations. TP53 was mutated in 20/21 (95.2%) of tissue samples and in 15/21 (71.4%) corresponding plasma samples at BL. Therefore, TP53 mutations were used as a molecular marker of circulating tumor DNA levels post-surgery. In the remaining 5 BL cases the TP53 mutations were either not present in plasma (N= 3) or rested below the detection limit (N= 2). In d1, d4 and d10 post-surgical samples, the sample specific TP53 mutations were detected in 12 out of 15, 10 out of 14 and in 7 out of 13 cases, respectively. TP53variant allele frequency (VAF) did not differ among TR0 and TR>0 at BL (mean= 1.91 versus 1.73, Mann-Whitney test p = 0.86) whereas it was significantly lower for TR0 at d1 (mean= 0.06 versus 2,06; p value= 0.002), d4 (mean= 0.07 versus 1.8; p= 0.04) and d10 (mean VAF= 0 versus 1.04; p= 0.008). Five out of 9 TR>0 cases showed at least one increase in VAF between d0 and any additional time-point. In 8 out of 9 mutations remained detectable at d10 (VAF: 0.076 – 3.26). By contrast, TR0 cases showed consistent reduction in VAF throughout the follow-up period which maximized at d10. Conclusions: Liquid biopsycan efficiently detect somatic mutations in the cfDNA of pts with HGOC following debulking surgery. Variation of the TP53 VAF in sequential post-surgical samples appears to be restricted to TR>0 cases, whereas in TR0 pts VAF progressively decreases. Liquid biopsy may hold promise as a tool for the objective determination of residual disease after debulking surgery.
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Affiliation(s)
- Florian Heitz
- Department of Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | | | | | - Jalid Sehouli
- AGO and Charité Campus Virchow-Klinikum, Berlin, Germany
| | | | - Mareike Sprokmann
- Kliniken Essen-Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | | | - Beyhan Ataseven
- Department of Gynecology, Klinikum Essen Mitte, Essen, Germany
| | | | - Stephanie Schneider
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | | | | | - Sonia Prader
- Kliniken Essen-Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | | | - Alexandra Hengsbach
- Kliniken Essen-Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | | | - Elena Ioana Braicu
- Charité Universitätsmedizin Berlin, Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité Campus Virchow-Klinikum, Berlin, Germany
| | - Lukas C. Heukamp
- Haematopathology Hamburg and NEO New Oncology GmbH, Hamburg, Germany
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Menon R, Müller JN, Falk M, Lakis S, Mariotti E, Leenders F, Bertrand M, Neemann N, Netchaeva M, Heukamp LC, Gloeckner C, Tiemann M, Heuckmann J, Griesinger F. Concordance between comprehensive cancer genome profiling in plasma and matched tumor specimens. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e23146] [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
e23146 Background: The importance and clinical use of liquid biopsies to identify somatic, targetable alterations in the plasma of cancer patients is steadily increasing. However, their concordance with alterations identified in cancer specimens tested in routine diagnostics is not being monitored. In a cohort of non-squamous cell lung cancer patients, our aim was to systematically compare alterations found by a massively parallel sequencing liquid biopsy assay covering 39 cancer related genes (NEOliquid) with alterations identified by routine diagnostics in a certified central pathology laboratory. Methods: Routine Diagnostics: DNA mutational analysis was performed using cobas or Sanger-Sequencing. Rearrangements were identified using immunohistochemistry or FISH. NEOliquid assay: Cell-free DNA from plasma was subjected to hybrid-capture based next-generation sequencing to detect point mutations, small insertions and deletions, copy number alterations and genomic translocations in 39 clinically relevant genes in a single assay. To evaluate and compare the performance of liquid biopsies, we applied the NEOliquid tests on blood samples of 82 non-squamous NSCLC patients and correlated them with results of routine diagnostics of matched tissue samples. Results: Routine diagnostics for lung cancer related oncogenes (EGFR, ALK, ROS1, KRAS, BRAF) identified a total of 50 somatic alterations of which 37 were point mutations, 11 InDels and 2 gene fusions. NEOliquid analysis of the corresponding plasma sample revealed a total of 34 alterations, including 21 targetable driver alterations. Overall, the concordance of mutation calls between routine diagnostic testing and NEOliquid was 97.6%, with a sensitivity of > 70% and a specificity of 100%. Importantly, NEOliquid identified additional clinically relevant genomic alterations, not covered by routine testing. Conclusions: We have shown high concordance of genomic alterations identified from liquid biopsies and tumor tissue specimens. The excellent specificity of actionable alterations identified by NEOliquid offers analytical performance for routine diagnostic use.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lukas C. Heukamp
- Haematopathology Hamburg and NEO New Oncology GmbH, Hamburg, Germany
| | | | | | | | - Frank Griesinger
- Pius Hospital Oldenburg, University of Oldenburg, Oldenburg, Germany
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Lakis S, Mueller J, Bertrand M, Heuckmann J, Menon R, Netchaeva M, Roeper J, Heukamp L, Griesinger F. Detection of activating EGFR and KRAS mutations in a single liquid biopsy from a patient with adenocarcinoma of the lung using hybrid capture based sequencing. Pneumologie 2017. [DOI: 10.1055/s-0037-1598273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | | | | | | | | | - J Roeper
- Pius-Hospital, Universität Oldenburg
| | | | - F Griesinger
- Department of Hematology and Oncology, Pius-Hospital Oldenburg, University Hospital
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38
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Menon R, Mariotti E, Mueller J, Lakis S, Walsch N, Crown J, Heuckmann J, Griesinger F, Heukamp L. PUB053 Panel Based Hybrid Capture Sequencing Assay to Correlate Mutational Load with Response to Immunotherapy. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.2023] [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: 10/20/2022]
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39
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Menon R, Mueller J, Lakis S, Hube A, Bochtler T, Wesseler C, Griesinger F, Loeffler H, Langenbuch T, Brandts C, Garcia A, Krämer A, Heuckmann J, Heukamp L. Identification of therapeutically targetable genomic alterations in a cohort of patients with CUP using a hybrid-capture based next generation sequencing assay. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32751-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Müller J, Lakis S, Mariotti E, Schneider P, Glöckner C, Leenders F, Hube A, Gullo G, Crown J, Griesinger F, Heuckmann J, Heukamp L, Menon R. Hybrid-capture based sequencing assays to detect novel alterations in BRAF from tissue and liquid biopsies. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw380.18] [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: 11/12/2022] Open
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42
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Rosoux A, Pauwels P, Duplaquet F, D'Haene N, Weynand B, Delos M, Menon R, Heukamp LC, Thunnissen E, Ocak S. Effectiveness of crizotinib in a patient with ALK IHC-positive/FISH-negative metastatic lung adenocarcinoma. Lung Cancer 2016; 98:118-121. [PMID: 27393517 DOI: 10.1016/j.lungcan.2016.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 04/11/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 11/30/2022]
Abstract
We report a case of crizotinib effectiveness in a heavily pretreated patient with a metastatic NSCLC initially considered IHC-positive and FISH-negative for ALK rearrangement. After repeated analyses of tumor samples, borderline ALK FISH-positivity (18.5% positive cells) was demonstrated.
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Affiliation(s)
- A Rosoux
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium
| | - P Pauwels
- Center for Oncologic Research (CORE), Antwerp University, Antwerp, Belgium
| | - F Duplaquet
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium
| | - N D'Haene
- Department of Pathology, Université Libre de Bruxelles (ULB), Hôpital Erasme, Brussels, Belgium
| | - B Weynand
- Department of pathology, UZ Leuven, Leuven, Belgium
| | - M Delos
- Department of Pathology, UCL, CHU UCL Namur, Yvoir, Belgium
| | - R Menon
- Neo New Oncology GmbH, Cologne, Germany
| | | | - E Thunnissen
- Department of Pathology, VU University, Amsterdam, Netherlands
| | - S Ocak
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium.
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43
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Belliveau J, Menon R. SU-G-TeP3-12: Retrospective Assessment of R2star Using Ultra-High Field MRI in a Rodent Model of Radiation Necrosis. Med Phys 2016. [DOI: 10.1118/1.4957092] [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: 11/07/2022] Open
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44
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Heukamp LC, Menon R, Mueller J, Lakis S, Schulte J, Wiest G, Griesinger F, Salat C, Dziadziuszko R, Gautschi O, Grohe C, Crown J, Heuckmann J. Detection of actionable genome alterations using hybrid capture based next generation sequencing technology: NEOplus and NEOliquid. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Johannes Schulte
- Paediatric Oncology and Hematology Charité, University Hospital Berlin, Berlin, Germany
| | | | - Frank Griesinger
- Pius-Hospital Oldenburg, University of Oldenburg, Oldenburg, Germany
| | | | | | - Oliver Gautschi
- Cantonal Hospital Lucerne and Swiss Group for Clinical Cancer Research (SAKK), Luzern, Switzerland
| | | | - John Crown
- Irish Cooperative Oncology Research Group, Dublin, Ireland
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45
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Shen J, Serby M, Reed A, Lee AJ, Menon R, Zhang X, Marsh K, Wan X, Kavetskaia O, Fischer V. Metabolism and Disposition of Hepatitis C Polymerase Inhibitor Dasabuvir in Humans. Drug Metab Dispos 2016; 44:1139-47. [DOI: 10.1124/dmd.115.067512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/12/2016] [Indexed: 11/22/2022] Open
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46
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Menon R, Müller J, Schneider P, Lakis S, Thress K, Wolf J, Heukamp L, Heuckmann JM, Griesinger F. A Novel EGFR(C797) Variant Detected in a Pleural Biopsy Specimen from an Osimertinib-Treated Patient Using a Comprehensive Hybrid Capture-Based Next-Generation Sequencing Assay. J Thorac Oncol 2016; 11:e105-7. [PMID: 27086175 DOI: 10.1016/j.jtho.2016.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 10/21/2022]
Affiliation(s)
| | | | | | | | - Kenneth Thress
- Translational Science, Oncology iMED, AstraZeneca, Waltham, Massachusetts
| | - Jürgen Wolf
- Center for Integrated Oncology Köln Bonn, University Hospital of Cologne, Cologne, Germany
| | | | | | - Frank Griesinger
- Department of Hematology and Oncology, Pius Hospital, Oldenburg, Germany
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Heukamp L, Menon R, Müller J, Lakis S, Netchaeva M, Griesinger F, Eberhardt W, Heuckmann J. 65P NEOliquid: Detection of KIF5B–RET fusions in liquid biopsy samples. J Thorac Oncol 2016. [DOI: 10.1016/s1556-0864(16)30178-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rooney C, Geh C, Williams V, Heuckmann JM, Menon R, Schneider P, Al-Kadhimi K, Dymond M, Smith NR, Baker D, French T, Smith PD, Harrington EA, Barrett JC, Kilgour E. Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon. PLoS One 2016; 11:e0149628. [PMID: 26905262 PMCID: PMC4764357 DOI: 10.1371/journal.pone.0149628] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/03/2016] [Indexed: 12/24/2022] Open
Abstract
FGFR1 amplification occurs in ~20% of sqNSCLC and trials with FGFR inhibitors have selected FGFR1 amplified patients by FISH. Lung cancer cell lines were profiled for sensitivity to AZD4547, a potent, selective inhibitor of FGFRs 1–3. Sensitivity to FGFR inhibition was associated with but not wholly predicted by increased FGFR1 gene copy number. Additional biomarker assays evaluating expression of FGFRs and correlation between amplification and expression in clinical tissues are therefore warranted. We validated nanoString for mRNA expression analysis of 194 genes, including FGFRs, from clinical tumour tissue. In a panel of sqNSCLC tumours 14.4% (13/90) were FGFR1 amplified by FISH. Although mean FGFR1 expression was significantly higher in amplified samples, there was significant overlap in the range of expression levels between the amplified and non-amplified cohorts with several non-amplified samples expressing FGFR1 to levels equivalent to amplified samples. Statistical analysis revealed increased expression of FGFR1 neighboring genes on the 8p12 amplicon (BAG4, LSM1 and WHSC1L1) in FGFR1 amplified tumours, suggesting a broad rather than focal amplicon and raises the potential for codependencies. High resolution aCGH analysis of pre-clinical and clinical samples supported the presence of a broad and heterogeneous amplicon around the FGFR1 locus. In conclusion, the range of FGFR1 expression levels in both FGFR1 amplified and non-amplified NSCLC tissues, together with the breadth and intra-patient heterogeneity of the 8p amplicon highlights the need for gene expression analysis of clinical samples to inform the understanding of determinants of response to FGFR inhibitors. In this respect the nanoString platform provides an attractive option for RNA analysis of FFPE clinical samples.
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Affiliation(s)
- Claire Rooney
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
- * E-mail:
| | - Catherine Geh
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | - Victoria Williams
- AstraZeneca, Personalised Healthcare and Biomarkers Innovative Medicines, Alderley Park, Macclesfield and Melbourn, Cambridge, United Kingdom
| | | | | | | | - Katherine Al-Kadhimi
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | - Michael Dymond
- AstraZeneca, Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | - Neil R. Smith
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | - Dawn Baker
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | - Tim French
- AstraZeneca, Personalised Healthcare and Biomarkers Innovative Medicines, Alderley Park, Macclesfield and Melbourn, Cambridge, United Kingdom
| | - Paul D. Smith
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
| | | | - J. Carl Barrett
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts, United States of America
| | - Elaine Kilgour
- AstraZeneca, Oncology Innovative Medicines, Alderley Park, Macclesfield, United Kingdom
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Polettini J, Dutta E, Behnia F, Saade G, Torloni M, Menon R. Aging of intrauterine tissues in spontaneous preterm birth and preterm premature rupture of the membranes: A systematic review of the literature. Placenta 2015; 36:969-73. [DOI: 10.1016/j.placenta.2015.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/13/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
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Peifer M, Roels F, Hertwig F, Menon R, Kraemer A, Buettner R, Perner S, Schramm A, Schulte JH, Westermann F, Thomas RK, Fischer M. Abstract LB-210: Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Neuroblastoma is a malignant pediatric tumor of the sympathetic nervous system. While roughly half of these tumors regress spontaneously or are cured by limited therapy, high-risk neuroblastomas have an unfavorable clinical course, despite intensive multimodal treatment. The genetic basis of the various clinical subtypes of the disease has remained largely elusive. To gain a better understanding of the genetic events that may drive neuroblastoma tumorigenesis, we here performed whole-genome sequencing of 42 primary neuroblastomas (high-risk, n = 25; low-risk, n = 17). We identified genomic rearrangements affecting chromosome 5p15.22 in a 50 kb region centromeric of the human telomerase reverse transcriptase gene (TERT) in 8 tumors. The rearrangements occurred only in high-risk neuroblastomas (8/25, 32%) in mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumor type. In an Independent validation cohort of 14 high-risk neuroblastomas, we detected rearrangements of the TERT locus in 4 additional samples. The structure of the rearrangements varied greatly, including balanced translocations, low-level copy number gains, focal amplifications and chromothripsis. Independent of the copy number at this region, all alterations consistently induced massive transcriptional up-regulation of TERT and of three additional genes located in close proximity to the chromosomal breakpoint. By contrast, MYCN-amplified tumors showed only up-regulation of TERT itself, suggesting that both MYCN amplification and TERT rearrangements converge on TERT activation. Supporting a functional role of TERT, both MYCN-amplified neuroblastoma cell lines and cell lines bearing TERT rearrangements exhibited elevated TERT expression and enzymatic telomerase activity in comparison to cell lines without these aberrations. Our findings show that remodeling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma, and places telomerase activation in the center of transformation in a large fraction of these tumors. More broadly, our findings provide a mechanistic basis for molecular diagnosis and therapy of this deadly pediatric tumor entity.
Citation Format: Martin Peifer, Frederik Roels, Falk Hertwig, Roopika Menon, Andrea Kraemer, Reinhard Buettner, Sven Perner, Alexander Schramm, Johannes H. Schulte, Frank Westermann, Roman K. Thomas, Matthias Fischer. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-210. doi:10.1158/1538-7445.AM2015-LB-210
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Affiliation(s)
| | | | - Falk Hertwig
- 2University Hospital of Cologne, Cologne, Germany
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