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Tanaka Y, Mizuguchi R, Koseki N, Suzuki H, Suzuki T. Quality assessment of enzymatic methyl-seq library constructed using crude cell lysate. Biochem Biophys Res Commun 2024; 696:149488. [PMID: 38219485 DOI: 10.1016/j.bbrc.2024.149488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Enzymatic methyl-seq (EM-seq), an enzyme-based method, identifies genome-wide DNA methylation, which enables us to obtain reliable methylome data from purified genomic DNA by avoiding bisulfite-induced DNA damage. However, the loss of DNA during purification hinders the methylome analysis of limited samples. The crude DNA extraction method is the quickest and minimal sample loss approach for obtaining useable DNA without requiring additional dissolution and purification. However, it remains unclear whether crude DNA can be used directly for EM-seq library construction. In this study, we aimed to assess the quality of EM-seq libraries prepared directly using crude DNA. The crude DNA-derived libraries provided appropriate fragment sizes and concentrations for sequencing similar to those of the purified DNA-derived libraries. However, the sequencing results of crude samples exhibited lower reference sequence mapping efficiencies than those of the purified samples. Additionally, the lower-input crude DNA-derived sample exhibited a marginally lower cytosine-to-thymine conversion efficiency and hypermethylated pattern around gene regulatory elements than the higher-input crude DNA- or purified DNA-derived samples. In contrast, the methylation profiles of the crude and purified samples exhibited a significant correlation. Our findings indicate that crude DNA can be used as a raw material for EM-seq library construction.
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Affiliation(s)
- Yuki Tanaka
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Risa Mizuguchi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Norio Koseki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Takahiro Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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Irikura T, Fukuoka K, Nakazawa A, Ichimura K, Kurihara J, Koh K. Molecular characterization of long-term survivors of metastatic medulloblastoma treated with reduced-dose craniospinal irradiation. Childs Nerv Syst 2023; 39:2505-2507. [PMID: 37185696 DOI: 10.1007/s00381-023-05971-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS Current standard treatment for metastatic medulloblastoma consists of 36 Gray (Gy) of craniospinal irradiation (CSI) supplemented with local irradiation and adjuvant chemotherapy after surgery. Although contemporary protocols have been designed to limit a radiation dose using risk-adapted CSI dosing to reduce neurocognitive morbidity, high-dose CSI remains the standard of care. Recently, the molecular classification of medulloblastoma has been emerging but its clinical significance has not been established particularly in patients with metastatic medulloblastoma treated with lower dose of CSI. METHODS We molecularly analyzed three cases of metastatic medulloblastoma treated with 24.0 Gy of CSI by DNA methylation analysis using the Illumina EPIC array. RESULTS All three patients had spinal metastases at the time of diagnosis. Postoperative treatment included multiple courses of chemotherapy, 24 Gy of CSI with focal boost to primary and metastatic sites, and high-dose chemotherapy. There was no disease progression observed during the 9.0, 7.7, and 5.7 years post-diagnosis follow-up. The molecular diagnosis was Group 3/4 in all three cases. Cases 1 and 2 belonged to Subtypes 7 and 4, both of which were reported to be good prognostic subtypes among the group. Case 3 belonged to Subtype 5 with MYC amplification. CONCLUSIONS The present cases suggest that the novel subtype classification in Group 3/4 medulloblastoma may be useful for risk stratification of patients with metastatic medulloblastoma who received lower dose of CSI than standard treatment.
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Affiliation(s)
- Tomoya Irikura
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Kohei Fukuoka
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan.
| | - Atsuko Nakazawa
- Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Jun Kurihara
- Department of Neurosurgery, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
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Li Z, Zhou X, Liao D, Liu R, Zhao X, Wang J, Zhong Q, Zeng Z, Peng Y, Tan Y, Yang Z. Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials. Front Cell Infect Microbiol 2023; 13:1180194. [PMID: 37662009 PMCID: PMC10471985 DOI: 10.3389/fcimb.2023.1180194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations. Methods This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted. Results General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies. Disucssion This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.
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Affiliation(s)
- Zijiao Li
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xiang Zhou
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Danxi Liao
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Ruolan Liu
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xia Zhao
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zhuo Zeng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yizhi Peng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zichen Yang
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
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4
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Colin E, Duffourd Y, Tisserant E, Relator R, Bruel AL, Tran Mau-Them F, Denommé-Pichon AS, Safraou H, Delanne J, Jean-Marçais N, Keren B, Isidor B, Vincent M, Mignot C, Heron D, Afenjar A, Heide S, Faudet A, Charles P, Odent S, Herenger Y, Sorlin A, Moutton S, Kerkhof J, McConkey H, Chevarin M, Poë C, Couturier V, Bourgeois V, Callier P, Boland A, Olaso R, Philippe C, Sadikovic B, Thauvin-Robinet C, Faivre L, Deleuze JF, Vitobello A. OMIXCARE: OMICS technologies solved about 33% of the patients with heterogeneous rare neuro-developmental disorders and negative exome sequencing results and identified 13% additional candidate variants. Front Cell Dev Biol 2022; 10:1021785. [PMID: 36393831 PMCID: PMC9650323 DOI: 10.3389/fcell.2022.1021785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 07/28/2023] Open
Abstract
Purpose: Patients with rare or ultra-rare genetic diseases, which affect 350 million people worldwide, may experience a diagnostic odyssey. High-throughput sequencing leads to an etiological diagnosis in up to 50% of individuals with heterogeneous neurodevelopmental or malformation disorders. There is a growing interest in additional omics technologies in translational research settings to examine the remaining unsolved cases. Methods: We gathered 30 individuals with malformation syndromes and/or severe neurodevelopmental disorders with negative trio exome sequencing and array comparative genomic hybridization results through a multicenter project. We applied short-read genome sequencing, total RNA sequencing, and DNA methylation analysis, in that order, as complementary translational research tools for a molecular diagnosis. Results: The cohort was mainly composed of pediatric individuals with a median age of 13.7 years (4 years and 6 months to 35 years and 1 month). Genome sequencing alone identified at least one variant with a high level of evidence of pathogenicity in 8/30 individuals (26.7%) and at least a candidate disease-causing variant in 7/30 other individuals (23.3%). RNA-seq data in 23 individuals allowed two additional individuals (8.7%) to be diagnosed, confirming the implication of two pathogenic variants (8.7%), and excluding one candidate variant (4.3%). Finally, DNA methylation analysis confirmed one diagnosis identified by genome sequencing (Kabuki syndrome) and identified an episignature compatible with a BAFopathy in a patient with a clinical diagnosis of Coffin-Siris with negative genome and RNA-seq results in blood. Conclusion: Overall, our integrated genome, transcriptome, and DNA methylation analysis solved 10/30 (33.3%) cases and identified a strong candidate gene in 4/30 (13.3%) of the patients with rare neurodevelopmental disorders and negative exome sequencing results.
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Affiliation(s)
- Estelle Colin
- Service de Génétique Médicale, CHU d’Angers, Angers, France
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Emilie Tisserant
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
| | - Raissa Relator
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph’s Healthcare, London, ON, Canada
| | - Ange-Line Bruel
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frédéric Tran Mau-Them
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Hana Safraou
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Centre de Génétique et Centre de Référence “Anomalies du Développement et Syndromes Malformatifs”, Hôpital d’Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence “Anomalies du Développement et Syndromes Malformatifs”, Hôpital d’Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Boris Keren
- Assistance publique - Hôpitaux de Paris (APHP), Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Cyril Mignot
- Sorbonne Université/INSERM U1127/CNRS UMR 7225/Institut du Cerveau, Paris, France
- Service de Neurologie, Hôpital la Pitié Salpêtrière, Sorbonne Université, Paris, France
| | - Delphine Heron
- Département de Génétique, Assistance publique - Hôpitaux de Paris Sorbonne Université, Hôpital Pitié-Salpêtrière et Trousseau, Paris, France
| | - Alexandra Afenjar
- Assistance publique - Hôpitaux de Paris, Département de Génétique, Sorbonne Université, GRC No. 19, ConCer-LD, Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital Armand Trousseau, Paris, France
| | - Solveig Heide
- Département de Génétique, Assistance publique - Hôpitaux de Paris Sorbonne Université, Hôpital Pitié-Salpêtrière et Trousseau, Paris, France
| | - Anne Faudet
- Département de Génétique, Assistance publique - Hôpitaux de Paris Sorbonne Université, Hôpital Pitié-Salpêtrière et Trousseau, Paris, France
| | - Perrine Charles
- Département de Génétique, Assistance publique - Hôpitaux de Paris Sorbonne Université, Hôpital Pitié-Salpêtrière et Trousseau, Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, European Reference Network (ERN) ITHACA, CHU Rennes, Rennes, France
- IGDR (Institut de Génétique et Développement de Rennes)—UMR 6290, ERL U1305, CNRS, INSERM, Univ Rennes, Rennes, France
| | - Yvan Herenger
- Service de Génétique Médicale, CHU de Tours, Tours, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence “Anomalies du Développement et Syndromes Malformatifs”, Hôpital d’Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence “Anomalies du Développement et Syndromes Malformatifs”, Hôpital d’Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph’s Healthcare, London, ON, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph’s Healthcare, London, ON, Canada
| | - Martin Chevarin
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Charlotte Poë
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Victor Couturier
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Valentin Bourgeois
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Patrick Callier
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
| | - Anne Boland
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
- LabEx GENMED (Medical Genomics)ParisFrance
| | - Christophe Philippe
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph’s Healthcare, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Christel Thauvin-Robinet
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Centre de Référence Maladies Rares “Déficiences Intellectuelles de Causes Rares”, Centre de Génétique, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Centre de Génétique et Centre de Référence “Anomalies du Développement et Syndromes Malformatifs”, Hôpital d’Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Jean-François Deleuze
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
- LabEx GENMED (Medical Genomics)ParisFrance
| | - Antonio Vitobello
- UFR des Sciences de Santé, GAD “Génétique des Anomalies du Développement”, INSERM-Université de Bourgogne UMR1231, Fédération Hospitalo-Universitaire (FHU)-TRANSLAD, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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5
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Reinhardt A, Pfister K, Schrimpf D, Stichel D, Sahm F, Reuss DE, Capper D, Wefers AK, Ebrahimi A, Sill M, Felsberg J, Reifenberger G, Becker A, Prinz M, Staszewski O, Hartmann C, Schittenhelm J, Gramatzki D, Weller M, Olar A, Rushing EJ, Bergmann M, Farrell MA, Blümcke I, Coras R, Beckervordersandforth J, Kim SH, Rogerio F, Dimova PS, Niehusmann P, Unterberg A, Platten M, Pfister SM, Wick W, Herold-Mende C, von Deimling A. Anaplastic ganglioglioma - a diagnosis comprising several distinct tumour types. Neuropathol Appl Neurobiol 2022; 48:e12847. [PMID: 35977725 DOI: 10.1111/nan.12847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/20/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Anaplastic ganglioglioma is a rare tumour and diagnosis has been based on histological criteria. The 5th edition of the World Health Organization Classification of Tumours of the Central Nervous System (CNS WHO) does not list anaplastic ganglioglioma as a distinct diagnosis due to lack of molecular data in previous publications AIM: We retrospectively compiled a cohort of 54 histologically diagnosed anaplastic gangliogliomas to explore whether the molecular profiles of these tumours represent a separate type or resolve into other entities METHODS: Samples were subjected to histological review, DNA methylation profiling and next generation sequencing. Morphologic and molecular data were summarised to an integrated diagnosis RESULTS: The majority of histologically diagnosed anaplastic gangliogliomas resolved into CNS WHO diagnoses of glial tumours, most commonly pleomorphic xanthoastrocytoma (16/54), glioblastoma, IDH wildtype and diffuse paediatric-type high-grade glioma, H3 wildtype and IDH wildtype (11 and 2/54) followed by low-grade glial or glioneuronal tumours including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumour and diffuse leptomeningeal glioneuronal tumour (5/54), IDH mutant astrocytoma (4/54) and others (6/54). A subset of tumours (10/54) was not assignable to a CNS WHO diagnosis and common molecular profiles pointing to a separate entity were not evident CONCLUSION: In summary, we show that tumours histologically diagnosed as anaplastic ganglioglioma comprise a wide spectrum of CNS WHO tumour types with different prognostic and therapeutic implications. We therefore suggest assigning this designation with caution and recommend comprehensive molecular workup.
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Affiliation(s)
- Annekathrin Reinhardt
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Current address: Centre for Human Genetics Tübingen, Tübingen, Germany
| | - Kristin Pfister
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Kantonsspital Winterthur, Winterthur, Switzerland
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Martin Sill
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Joerg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ori Staszewski
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School, Hannover, Germany
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, University Tübingen, Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital and University Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University Zurich, Zurich, Switzerland
| | | | | | - Markus Bergmann
- Institute of Neuropathology, Center for Pathology, Klinikum Bremen Mitte, Bremen, Germany
| | | | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Roland Coras
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Jan Beckervordersandforth
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Se Hoon Kim
- Department of Pathology, Yonsei University, College of Medicine, Seoul, South Korea
| | - Fabio Rogerio
- Department of Pathology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Petia S Dimova
- Epilepsy Surgery Center, Department of Neurosurgery, St. Ivan Rilski University Hospital, Sofia, Bulgaria
| | - Pitt Niehusmann
- Section of Neuropathology, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Andreas Unterberg
- Clinic for Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumour Immunology, German Cancer Research Center (DKFZ), Heidelberg
| | - Stefan M Pfister
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Paediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Neurology Clinic, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
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6
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Gutierrez J, Davis BA, Nevonen KA, Ward S, Carbone L, Maslen CL. DNA Methylation Analysis of Turner Syndrome BAV. Front Genet 2022; 13:872750. [PMID: 35711915 PMCID: PMC9194862 DOI: 10.3389/fgene.2022.872750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022] Open
Abstract
Turner Syndrome (TS) is a rare cytogenetic disorder caused by the complete loss or structural variation of the second sex chromosome. The most common cause of early mortality in TS results from a high incidence of left-sided congenital heart defects, including bicuspid aortic valve (BAV), which occurs in about 30% of individuals with TS. BAV is also the most common congenital heart defect in the general population with a prevalence of 0.5–2%, with males being three-times more likely to have a BAV than females. TS is associated with genome-wide hypomethylation when compared to karyotypically normal males and females. Alterations in DNA methylation in primary aortic tissue are associated with BAV in euploid individuals. Here we show significant differences in DNA methylation patterns associated with BAV in TS found in peripheral blood by comparing TS BAV (n = 12), TS TAV (n = 13), and non-syndromic BAV (n = 6). When comparing TS with BAV to TS with no heart defects we identified a differentially methylated region encompassing the BAV-associated gene MYRF, and enrichment for binding sites of two known transcription factor contributors to BAV. When comparing TS with BAV to euploid women with BAV, we found significant overlapping enrichment for ChIP-seq transcription factor targets including genes in the NOTCH1 pathway, known for involvement in the etiology of non-syndromic BAV, and other genes that are essential regulators of heart valve development. Overall, these findings suggest that altered DNA methylation affecting key aortic valve development genes contributes to the greatly increased risk for BAV in TS.
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Affiliation(s)
- Jacob Gutierrez
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Brett A Davis
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Kimberly A Nevonen
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Samantha Ward
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Lucia Carbone
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States.,Department of Medicine, Oregon Health and Science University, Portland, OR, United States.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, United States
| | - Cheryl L Maslen
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, United States
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7
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Zuccato JA, Patil V, Mansouri S, Liu JC, Nassiri F, Mamatjan Y, Chakravarthy A, Karimi S, Almeida JP, Bernat AL, Hasen M, Singh O, Khan S, Kislinger T, Sinha N, Froelich S, Adle-Biassette H, Aldape KD, De Carvalho DD, Zadeh G. DNA Methylation based prognostic subtypes of chordoma tumors in tissue and plasma. Neuro Oncol 2021; 24:442-454. [PMID: 34614192 DOI: 10.1093/neuonc/noab235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chordomas are rare malignant bone cancers of the skull-base and spine. Patient survival is variable and not reliably predicted using clinical factors or molecular features. This study identifies prognostic epigenetic chordoma subtypes that are detected non-invasively using plasma methylomes. METHODS Methylation profiles of 68 chordoma surgical samples were obtained between 1996-2018 across three international centres along with matched plasma methylomes where available. RESULTS Consensus clustering identified two stable tissue clusters with a disease-specific survival difference that was independent of clinical factors in a multivariate Cox analysis (HR=14.2, 95%CI: 2.1-94.8, p=0.0063). Immune-related pathways with genes hypomethylated at promoters and increased immune cell abundance were observed in the poor-performing "Immune-infiltrated" subtype. Cell-to-cell interaction plus extracellular matrix pathway hypomethylation and higher tumor purity was observed in the better-performing "Cellular" subtype. The findings were validated in additional DNA methylation and RNA sequencing datasets as well as with immunohistochemical staining. Plasma methylomes distinguished chordomas from other clinical differential diagnoses by applying fifty chordoma-versus-other binomial generalized linear models in random 20% testing sets (mean AUROC=0.84, 95%CI: 0.52-1.00). Tissue-based and plasma-based methylation signals were highly correlated in both prognostic clusters. Additionally, leave-one-out models accurately classified all tumors into their correct cluster based on plasma methylation data. CONCLUSIONS Here, we show the first identification of prognostic epigenetic chordoma subtypes and first use of plasma methylome-based biomarkers to non-invasively diagnose and subtype chordomas. These results may transform patient management by allowing treatment aggressiveness to be balanced with patient risk according to prognosis.
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Affiliation(s)
- Jeffrey A Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Sheila Mansouri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shirin Karimi
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Joao Paulo Almeida
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Laure Bernat
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Mohammed Hasen
- Section of Neurosurgery, Division of Surgery, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada.,Department of Neurosurgery, King Fahad University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Namita Sinha
- Department of Pathology, Shared Health, HSC, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sébastien Froelich
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Homa Adle-Biassette
- Department of Pathology, Lariboisière Hospital, Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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8
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Kraus TFJ, Pöppe J, Machegger L, Zellinger B, Dovjak E, Schlicker HU, Schwartz C, Ladisich B, Spendel M, Al‐Schameri AR, Winkler PA, Sotlar K. Genotypical glioblastoma of the frontal lobe mimicking ganglioglioma: A case report and review of the literature. Clin Case Rep 2021; 9:e04544. [PMID: 34484744 PMCID: PMC8405366 DOI: 10.1002/ccr3.4544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/16/2021] [Indexed: 11/18/2022] Open
Abstract
This case of severe phenotype-genotype mismatch brain tumor morphologically mimicking benign ganglioglioma emphasizes the urgent need for advanced molecular profiling in brain tumor diagnosis in the era of sophisticated molecular profiling.
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Affiliation(s)
- Theo F. J. Kraus
- Institute of PathologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Johannes Pöppe
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Lukas Machegger
- Institute of NeuroradiologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Barbara Zellinger
- Institute of PathologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Eva Dovjak
- Institute of PathologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Hans U. Schlicker
- Institute of PathologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Christoph Schwartz
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Barbara Ladisich
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Mathias Spendel
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Abdul R. Al‐Schameri
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Peter A. Winkler
- Department of NeurosurgeryUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Karl Sotlar
- Institute of PathologyUniversity Hospital SalzburgParacelsus Medical UniversitySalzburgAustria
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9
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Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, Castro de Moura M, Esteller M, Shen H, Zenklusen JC, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, Ivy SP, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell 2021; 39:38-53.e7. [PMID: 33217343 PMCID: PMC8478080 DOI: 10.1016/j.ccell.2020.10.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022]
Abstract
A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
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Affiliation(s)
- David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alina M Hamilton
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Ninad Dewal
- Foundation Medicine Inc, Cambridge, MA 02141, USA
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08007 Barcelona, Catalonia, Spain
| | - Hui Shen
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lisa M McShane
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - James V Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul M Williams
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Irina Lubensky
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Elise C Kohn
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard F Little
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffrey White
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shakun Malik
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lyndsay Harris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carol Weil
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chris Karlovich
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian Rodgers
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lalitha Shankar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paula Jacobs
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracy Nolan
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Elijah F Edmondson
- Pathology and Histology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Barbara A Conley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - S Percy Ivy
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.
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10
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Kuwahara Y, Iehara T, Ichise E, Katsumi Y, Ouchi K, Tsuchiya K, Miyachi M, Konishi E, Sasajima H, Nakamura S, Fumino S, Tajiri T, Johann PD, FrÜhwald MC, Yoshida T, Okuda T, Hosoi H. Novel Two MRT Cell Lines Established from Multiple Sites of a Synchronous MRT Patient. Anticancer Res 2020; 40:6159-6170. [PMID: 33109553 DOI: 10.21873/anticanres.14636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Malignant rhabdoid tumor (MRT) is a rare, aggressive neoplasm found in young children, caused by inactivation of a single gene, SNF5 (INI1, SMARCB1). MRT cases with multifocal tumors at diagnosis are categorized as synchronous MRT, often with a germline mutation of SNF5. The aim of this study was to establish new models useful in clarifying the biological basis of synchronous MRT. MATERIALS AND METHODS We established two novel MRT cell lines, designated as KP-MRT-KS and KP-MRT-KSa, derived from different lesions and at a different time from a synchronous multifocal 7-month-old female MRT patient. RESULTS Both cells showed typical morphology of MRT, with a compound genomic mutation in exons 2 and 5 of the SNF5 gene. The exon 2 mutation was found in the germline. CONCLUSION These cell lines could serve as powerful tools for unveiling the molecular mechanism of refractory synchronous MRT.
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Affiliation(s)
- Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eisuke Ichise
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiki Katsumi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazutaka Ouchi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kunihiko Tsuchiya
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mitsuru Miyachi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eiichi Konishi
- Department of Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroyasu Sasajima
- Department of Neurosurgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Nakamura
- Department of Radiology, Kansai Medical University, Osaka, Japan
| | - Shigehisa Fumino
- Department of Pediatric Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Pascal D Johann
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael C FrÜhwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg, Germany
| | - Tatsushi Yoshida
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsukasa Okuda
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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11
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Gissi DB, Gabusi A, Tarsitano A, Rossi R, Balbi T, Morandi L. Multi-Region Sequence Analysis of a Pregnancy-Related Oral Squamous Cell Carcinoma Exhibiting Low-Level Aggressive Behavior. Int J Surg Pathol 2019; 28:188-195. [PMID: 31544567 DOI: 10.1177/1066896919876058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We analyzed the genetic and epigenetic profiles of an oral squamous cell carcinoma affecting a 41-year-old pregnant female. The patient presented with an oral mass located at the hard and soft palate with bone involvement and lymph node metastases (T4N1M0). She had been treated with multimodal radiotherapy and chemotherapy, and she is currently alive with no evidence of disease 8 years after treatment. DNA methylation and DNA mutation analyses were used to analyze multiple samples from the tumor mass and from the non-neoplastic mucosa to verify tumor heterogeneity. Genetic and epigenetic analyses revealed the presence of one shared TP53 driver mutation with the same DNA methylation profile in each of the 3 areas of the tumor mass; only 2 additional passenger mutations were detected, suggesting a simple clonal homogeneous carcinoma, which usually is associated with low-level aggressive behavior. Additionally, no genetic or epigenetic alteration in the non-neoplastic oral mucosa was detected, demonstrating the absence of field cancerization. The low aggressiveness of the lesion was confirmed by the patient being free of disease at a long-term follow-up examination. These data suggest a different molecular transformation pathway in pregnancy-related oral squamous cell carcinomas, providing new perspectives for further investigation.
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12
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Jeltsch A, Broche J, Lungu C, Bashtrykov P. Biotechnological Applications of MBD Domain Proteins for DNA Methylation Analysis. J Mol Biol 2019:S0022-2836(19)30544-3. [PMID: 31493411 DOI: 10.1016/j.jmb.2019.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 02/03/2023]
Abstract
5-Methylcytosine binding domain (MBD) family proteins are essential readers of DNA methylation. Their methylation specific DNA binding has been exploited in the context of two main groups of important biotechnological applications. In the first, an MBD domain is used to bind methylated DNA in vitro. This can be employed for global DNA methylation analysis in MBD-seq assays, where methylated DNA is purified from fragmented genomic DNA by MBD pulldown or capture, followed by next-generation sequencing (NGS) and downstream data analysis as established for ChIP-seq applications. In addition, the ability of MBD domains to bind methylated DNA can be used for in vitro DNMT activity and inhibition assays. In the second type of applications, MBD domains are used to bind methylated DNA in cells. In MBD imaging, these domains are fused to fluorophores and expressed in cells, where they bind to methylated DNA allowing the readout of DNA methylation by fluorescence microscopy. This approach recently has been further developed to allow the locus-specific readout of DNA methylation using bimolecular fluorescence complementation-based bimolecular anchor detector sensors. These tools, which are compatible with live cell imaging, combine the sequence-specific DNA binding of anchor domains and the 5-methylcytosine-specific binding of an MBD domain to chromatin. Depending on the individual assay, MBD-based detection systems for DNA methylation provide important advantages, ranging from cost efficiency and easy workflows to unique opportunities for the readout of methylation levels in living cells with locus-specific resolution during organismic development.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Cristiana Lungu
- Institute of Cell Biology and Immunology, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
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13
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Römer T, Temming P, Lohmann DR, Sturm D, von Deimling A, Sellhaus B, Mull M, Kontny U, Moser O. Ectopic intracranial retinoblastoma in a 3.5-month-old infant without eye involvement and without evidence of heritability. Pediatr Blood Cancer 2019; 66:e27599. [PMID: 30604586 DOI: 10.1002/pbc.27599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023]
Abstract
Heritable retinoblastoma can rarely be associated with a midline intracranial neuroblastic tumor, referred to as trilateral retinoblastoma. We present an unusual midline brain tumor in an infant that was identified as ectopic retinoblastoma by histopathology, DNA methylation analysis, and molecular genetic detection of biallelic somatic inactivation of the RB1 gene. There was no ocular involvement, and germline mutation was excluded. In this nonresectable tumor, treatment with systemic chemotherapy including high-dose therapy with autologous stem cell transplantation, but without definite local therapy, resulted in long-lasting tumor control.
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Affiliation(s)
- Tristan Römer
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Petra Temming
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital; and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Bernd Sellhaus
- Department of Neuropathology, RWTH Aachen University, Aachen, Germany
| | - Michael Mull
- Department of Diagnostic and Interventional Neuroradiology, RWTH Aachen University, Aachen, Germany
| | - Udo Kontny
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Olga Moser
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Signorile PG, Severino A, Santoro M, Spyrou M, Viceconte R, Baldi A. Methylation analysis of HOXA10 regulatory elements in patients with endometriosis. BMC Res Notes 2018; 11:722. [PMID: 30309386 PMCID: PMC6182800 DOI: 10.1186/s13104-018-3836-1] [Citation(s) in RCA: 5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/09/2018] [Indexed: 11/30/2022] Open
Abstract
Objective The pathogenesis of endometriosis is still mysterious, being retrograde menstruation and coelomic metaplasia the most accepted hypotheses. Recently, it has been proposed that endometriosis is caused by fine-tuning alterations of the female genital system development during the foetal life and that in utero exposition to endocrine disruptors can be one of the factors causing the disease, possibly acting on the methylation status of the genome. In this study, we have evaluated the methylation status of HOXA10 gene regulation regions in a cohort of 22 endometriosis patients respect to a control group of 6 healthy women. Results The methylation study was carried out on three CpG islands, previously described hypermethylated in the endometrium of endometriosis patients and include 22 CpG sites, 21 CpG sites and 10 CpG sites, respectively identified through the online platform MethPrimer. The analysis did not find significant differences between patients with endometriosis and healthy control individuals. These results confirm previous studies on genome wide methylation analysis in endometriosis patients. Therefore, other epigenetically altered genes should be considered more related to the pathogenesis of endometriosis.
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Affiliation(s)
| | - Anna Severino
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | | | | | | | - Alfonso Baldi
- Fondazione Italiana Endometriosi, Rome, Italy. .,Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "L. Vanvitelli", Caserta, Italy.
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15
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Affinito O, Scala G, Palumbo D, Florio E, Monticelli A, Miele G, Avvedimento VE, Usiello A, Chiariotti L, Cocozza S. Modeling DNA methylation by analyzing the individual configurations of single molecules. Epigenetics 2016; 11:881-888. [PMID: 27748645 DOI: 10.1080/15592294.2016.1246108] [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] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is often analyzed by reporting the average methylation degree of each cytosine. In this study, we used a single molecule methylation analysis in order to look at the methylation conformation of individual molecules. Using D-aspartate oxidase as a model gene, we performed an in-depth methylation analysis through the developmental stages of 3 different mouse tissues (brain, lung, and gut), where this gene undergoes opposite methylation destiny. This approach allowed us to track both methylation and demethylation processes at high resolution. The complexity of these dynamics was markedly simplified by introducing the concept of methylation classes (MCs), defined as the number of methylated cytosines per molecule, irrespective of their position. The MC concept smooths the stochasticity of the system, allowing a more deterministic description. In this framework, we also propose a mathematical model based on the Markov chain. This model aims to identify the transition probability of a molecule from one MC to another during methylation and demethylation processes. The results of our model suggest that: 1) both processes are ruled by a dominant class of phenomena, namely, the gain or loss of one methyl group at a time; and 2) the probability of a single CpG site becoming methylated or demethylated depends on the methylation status of the whole molecule at that time.
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Affiliation(s)
- Ornella Affinito
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Giovanni Scala
- c Istituto Nazionale di Fisica Nucleare , Sezione di Napoli , Naples , Italy
| | - Domenico Palumbo
- b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Ermanno Florio
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Antonella Monticelli
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy
| | - Gennaro Miele
- c Istituto Nazionale di Fisica Nucleare , Sezione di Napoli , Naples , Italy.,d Dipartimento di Fisica , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Vittorio Enrico Avvedimento
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Alessandro Usiello
- e CEINGE Biotecnologie Avanzate , Naples , Italy.,f Department of Environmental, Biological and Pharmaceutical Science and Technologies , Second University of Naples , Caserta , Italy
| | - Lorenzo Chiariotti
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy.,g Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Sergio Cocozza
- b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
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16
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Jeong HM, Lee S, Chae H, Kim R, Kwon MJ, Oh E, Choi YL, Kim S, Shin YK. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics 2016; 8:1061-77. [PMID: 27266718 DOI: 10.2217/epi-2016-0038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIMS We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. RESULTS MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. CONCLUSION MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.
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Affiliation(s)
- Hae Min Jeong
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sangseon Lee
- School of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea
| | - Heejoon Chae
- Computer Science Department, School of Informatics & Computing, Indiana University, Bloomington, IN, USA
| | - RyongNam Kim
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
| | - Ensel Oh
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics & Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Kim
- Department of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Young Kee Shin
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.,The Center for Anti-Cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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17
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Abstract
We report a unique amplification technique that works efficiently and specifically over a temperature range, rather than at one specific temperature, throughout the amplification process. As bisulfite-modified DNA is one of the difficult to amplify templates, we used this technique to amplify regions of promoter-associated CpG island for 11 genes using this template. This technique amplified specific products for every gene without requiring any optimization.
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Affiliation(s)
- F B Rowther
- Brain Tumour UK Neuro-oncology Research Centre, Research Institute in Healthcare Sciences, School of Applied Sciences, University of Wolverhampton, Wolverhampton, United Kingdom.
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