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Article ; Online: DLK1/DIO3 locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis.

Molecular therapy : the journal of the American Society of Gene Therapy

2024 Volume 32, Issue 4, Page(s) 1125–1143

Abstract: The CTNNB1 gene, encoding β-catenin, is frequently mutated in hepatocellular carcinoma (HCC, ∼30%) and in hepatoblastoma (HB, >80%), in which DLK1/DIO3 locus induction is correlated with CTNNB1 mutations. Here, we aim to decipher how sustained β-catenin ... ...

Abstract	The CTNNB1 gene, encoding β-catenin, is frequently mutated in hepatocellular carcinoma (HCC, ∼30%) and in hepatoblastoma (HB, >80%), in which DLK1/DIO3 locus induction is correlated with CTNNB1 mutations. Here, we aim to decipher how sustained β-catenin activation regulates DLK1/DIO3 locus expression and the role this locus plays in HB and HCC development in mouse models deleted for Apc (Apc
MeSH term(s)	Animals ; Humans ; Mice ; beta Catenin/genetics ; beta Catenin/metabolism ; Calcium-Binding Proteins/genetics ; Calcium-Binding Proteins/metabolism ; Carcinogenesis/genetics ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/metabolism ; Catenins/genetics ; Catenins/metabolism ; Cell Proliferation/genetics ; Liver Neoplasms/genetics ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Up-Regulation
Chemical Substances	beta Catenin ; Calcium-Binding Proteins ; Catenins ; DLK1 protein, human ; Membrane Proteins ; iodothyronine deiodinase type III (EC 1.11.1.-) ; CTNNB1 protein, human
Language	English
Publishing date	2024-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2024.01.036
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma.

Mauger, Florence / Dulary, Cécile / Daviaud, Christian / Deleuze, Jean-François / Tost, Jorg

Analytical and bioanalytical chemistry

2015 Volume 407, Issue 22, Page(s) 6873–6878

Abstract: Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics, and prediction and monitoring of treatment response, but its amount is usually limited. Therefore, the choice of methods to extract and characterize ccfDNA is crucial. ... ...

Abstract	Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics, and prediction and monitoring of treatment response, but its amount is usually limited. Therefore, the choice of methods to extract and characterize ccfDNA is crucial. In the current study, we performed the most comprehensive comparison of methods for ccfDNA extraction (11 methods), quantification (3 methods), and estimation of the integrity index (2 methods) from small quantities of different kinds of plasma. The QIAamp® Circulating Nucleic Acid Kit and the Norgen Plasma/Serum Circulating DNA Purification Mini Kit showed the best accuracy and reproducibility, but the Norgen kit allowed to extract a higher amount of ccfDNA. This workflow provides a reliable protocol for the multiple applications of ccfDNA in biomedicine.
MeSH term(s)	Aged ; Aged, 80 and over ; Base Sequence ; Cell-Free System ; DNA, Neoplasm/blood ; DNA, Neoplasm/genetics ; DNA, Neoplasm/isolation & purification ; Female ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods
Chemical Substances	DNA, Neoplasm
Language	English
Publishing date	2015-09
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-015-8846-4
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Article ; Online: White Blood Cell BRCA1 Promoter Methylation Status and Ovarian Cancer Risk.

Lønning, Per E / Berge, Elisabet O / Bjørnslett, Merete / Minsaas, Laura / Chrisanthar, Ranjan / Høberg-Vetti, Hildegunn / Dulary, Cécile / Busato, Florence / Bjørneklett, Silje / Eriksen, Christine / Kopperud, Reidun / Axcrona, Ulrika / Davidson, Ben / Bjørge, Line / Evans, Gareth / Howell, Anthony / Salvesen, Helga B / Janszky, Imre / Hveem, Kristian /

Romundstad, Pål R / Vatten, Lars J / Tost, Jörg / Dørum, Anne / Knappskog, Stian

Annals of internal medicine

2018 Volume 168, Issue 5, Page(s) 326–334

Abstract: Background: The role of normal tissue gene promoter methylation in cancer risk is poorly understood.: Objective: To assess associations between normal tissue BRCA1 methylation and ovarian cancer risk.: Design: 2 case-control (initial and ... ...

Abstract	Background: The role of normal tissue gene promoter methylation in cancer risk is poorly understood. Objective: To assess associations between normal tissue BRCA1 methylation and ovarian cancer risk. Design: 2 case-control (initial and validation) studies. Setting: 2 hospitals in Norway (patients) and a population-based study (control participants). Participants: 934 patients and 1698 control participants in the initial study; 607 patients and 1984 control participants in the validation study. Measurements: All patients had their blood sampled before chemotherapy. White blood cell (WBC) BRCA1 promoter methylation was determined by using methylation-specific quantitative polymerase chain reaction, and the percentage of methylation-positive samples was compared between population control participants and patients with ovarian cancer, including the subgroup with high-grade serous ovarian cancer (HGSOC). Results: In the initial study, BRCA1 methylation was more frequent in patients with ovarian cancer than control participants (6.4% vs. 4.2%; age-adjusted odds ratio [OR], 1.83 [95% CI, 1.27 to 2.63]). Elevated methylation, however, was restricted to patients with HGSOC (9.6%; OR, 2.91 [CI, 1.85 to 4.56]), in contrast to 5.1% and 4.0% of patients with nonserous and low-grade serous ovarian cancer (LGSOC), respectively. These findings were replicated in the validation study (methylation-positive status in 9.1% of patients with HGSOC vs. 4.3% of control participants-OR, 2.22 [CI 1.40 to 3.52]-4.1% of patients with nonserous ovarian cancer, and 2.7% of those with LGSOC). The results were not influenced by tumor burden, storage time, or WBC subfractions. In separate analyses of young women and newborns, BRCA1 methylation was detected in 4.1% (CI, 1.8% to 6.4%) and 7.0% (CI, 5.0% to 9.1%), respectively. Limitations: Patients with ovarian cancer were recruited at the time of diagnosis in a hospital setting. Conclusion: Constitutively normal tissue BRCA1 promoter methylation is positively associated with risk for HGSOC. Primary funding source: Norwegian Cancer Society.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; DNA Methylation ; Female ; Genes, BRCA1 ; Germ-Line Mutation ; Humans ; Infant, Newborn ; Leukocytes ; Middle Aged ; Norway ; Ovarian Neoplasms/chemistry ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; Risk
Language	English
Publishing date	2018-01-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/M17-0101
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Article ; Online: Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.

Sims, Rebecca / van der Lee, Sven J / Naj, Adam C / Bellenguez, Céline / Badarinarayan, Nandini / Jakobsdottir, Johanna / Kunkle, Brian W / Boland, Anne / Raybould, Rachel / Bis, Joshua C / Martin, Eden R / Grenier-Boley, Benjamin / Heilmann-Heimbach, Stefanie / Chouraki, Vincent / Kuzma, Amanda B / Sleegers, Kristel / Vronskaya, Maria / Ruiz, Agustin / Graham, Robert R /

Olaso, Robert / Hoffmann, Per / Grove, Megan L / Vardarajan, Badri N / Hiltunen, Mikko / Nöthen, Markus M / White, Charles C / Hamilton-Nelson, Kara L / Epelbaum, Jacques / Maier, Wolfgang / Choi, Seung-Hoan / Beecham, Gary W / Dulary, Cécile / Herms, Stefan / Smith, Albert V / Funk, Cory C / Derbois, Céline / Forstner, Andreas J / Ahmad, Shahzad / Li, Hongdong / Bacq, Delphine / Harold, Denise / Satizabal, Claudia L / Valladares, Otto / Squassina, Alessio / Thomas, Rhodri / Brody, Jennifer A / Qu, Liming / Sánchez-Juan, Pascual / Morgan, Taniesha / Wolters, Frank J / Zhao, Yi / Garcia, Florentino Sanchez / Denning, Nicola / Fornage, Myriam / Malamon, John / Naranjo, Maria Candida Deniz / Majounie, Elisa / Mosley, Thomas H / Dombroski, Beth / Wallon, David / Lupton, Michelle K / Dupuis, Josée / Whitehead, Patrice / Fratiglioni, Laura / Medway, Christopher / Jian, Xueqiu / Mukherjee, Shubhabrata / Keller, Lina / Brown, Kristelle / Lin, Honghuang / Cantwell, Laura B / Panza, Francesco / McGuinness, Bernadette / Moreno-Grau, Sonia / Burgess, Jeremy D / Solfrizzi, Vincenzo / Proitsi, Petra / Adams, Hieab H / Allen, Mariet / Seripa, Davide / Pastor, Pau / Cupples, L Adrienne / Price, Nathan D / Hannequin, Didier / Frank-García, Ana / Levy, Daniel / Chakrabarty, Paramita / Caffarra, Paolo / Giegling, Ina / Beiser, Alexa S / Giedraitis, Vilmantas / Hampel, Harald / Garcia, Melissa E / Wang, Xue / Lannfelt, Lars / Mecocci, Patrizia / Eiriksdottir, Gudny / Crane, Paul K / Pasquier, Florence / Boccardi, Virginia / Henández, Isabel / Barber, Robert C / Scherer, Martin / Tarraga, Lluis / Adams, Perrie M / Leber, Markus / Chen, Yuning / Albert, Marilyn S / Riedel-Heller, Steffi / Emilsson, Valur / Beekly, Duane / Braae, Anne / Schmidt, Reinhold / Blacker, Deborah / Masullo, Carlo / Schmidt, Helena / Doody, Rachelle S / Spalletta, Gianfranco / Longstreth, W T / Fairchild, Thomas J / Bossù, Paola / Lopez, Oscar L / Frosch, Matthew P / Sacchinelli, Eleonora / Ghetti, Bernardino / Yang, Qiong / Huebinger, Ryan M / Jessen, Frank / Li, Shuo / Kamboh, M Ilyas / Morris, John / Sotolongo-Grau, Oscar / Katz, Mindy J / Corcoran, Chris / Dunstan, Melanie / Braddel, Amy / Thomas, Charlene / Meggy, Alun / Marshall, Rachel / Gerrish, Amy / Chapman, Jade / Aguilar, Miquel / Taylor, Sarah / Hill, Matt / Fairén, Mònica Díez / Hodges, Angela / Vellas, Bruno / Soininen, Hilkka / Kloszewska, Iwona / Daniilidou, Makrina / Uphill, James / Patel, Yogen / Hughes, Joseph T / Lord, Jenny / Turton, James / Hartmann, Annette M / Cecchetti, Roberta / Fenoglio, Chiara / Serpente, Maria / Arcaro, Marina / Caltagirone, Carlo / Orfei, Maria Donata / Ciaramella, Antonio / Pichler, Sabrina / Mayhaus, Manuel / Gu, Wei / Lleó, Alberto / Fortea, Juan / Blesa, Rafael / Barber, Imelda S / Brookes, Keeley / Cupidi, Chiara / Maletta, Raffaele Giovanni / Carrell, David / Sorbi, Sandro / Moebus, Susanne / Urbano, Maria / Pilotto, Alberto / Kornhuber, Johannes / Bosco, Paolo / Todd, Stephen / Craig, David / Johnston, Janet / Gill, Michael / Lawlor, Brian / Lynch, Aoibhinn / Fox, Nick C / Hardy, John / Albin, Roger L / Apostolova, Liana G / Arnold, Steven E / Asthana, Sanjay / Atwood, Craig S / Baldwin, Clinton T / Barnes, Lisa L / Barral, Sandra / Beach, Thomas G / Becker, James T / Bigio, Eileen H / Bird, Thomas D / Boeve, Bradley F / Bowen, James D / Boxer, Adam / Burke, James R / Burns, Jeffrey M / Buxbaum, Joseph D / Cairns, Nigel J / Cao, Chuanhai / Carlson, Chris S / Carlsson, Cynthia M / Carney, Regina M / Carrasquillo, Minerva M / Carroll, Steven L / Diaz, Carolina Ceballos / Chui, Helena C / Clark, David G / Cribbs, David H / Crocco, Elizabeth A / DeCarli, Charles / Dick, Malcolm / Duara, Ranjan / Evans, Denis A / Faber, Kelley M / Fallon, Kenneth B / Fardo, David W / Farlow, Martin R / Ferris, Steven / Foroud, Tatiana M / Galasko, Douglas R / Gearing, Marla / Geschwind, Daniel H / Gilbert, John R / Graff-Radford, Neill R / Green, Robert C / Growdon, John H / Hamilton, Ronald L / Harrell, Lindy E / Honig, Lawrence S / Huentelman, Matthew J / Hulette, Christine M / Hyman, Bradley T / Jarvik, Gail P / Abner, Erin / Jin, Lee-Way / Jun, Gyungah / Karydas, Anna / Kaye, Jeffrey A / Kim, Ronald / Kowall, Neil W / Kramer, Joel H / LaFerla, Frank M / Lah, James J / Leverenz, James B / Levey, Allan I / Li, Ge / Lieberman, Andrew P / Lunetta, Kathryn L / Lyketsos, Constantine G / Marson, Daniel C / Martiniuk, Frank / Mash, Deborah C / Masliah, Eliezer / McCormick, Wayne C / McCurry, Susan M / McDavid, Andrew N / McKee, Ann C / Mesulam, Marsel / Miller, Bruce L / Miller, Carol A / Miller, Joshua W / Morris, John C / Murrell, Jill R / Myers, Amanda J / O'Bryant, Sid / Olichney, John M / Pankratz, Vernon S / Parisi, Joseph E / Paulson, Henry L / Perry, William / Peskind, Elaine / Pierce, Aimee / Poon, Wayne W / Potter, Huntington / Quinn, Joseph F / Raj, Ashok / Raskind, Murray / Reisberg, Barry / Reitz, Christiane / Ringman, John M / Roberson, Erik D / Rogaeva, Ekaterina / Rosen, Howard J / Rosenberg, Roger N / Sager, Mark A / Saykin, Andrew J / Schneider, Julie A / Schneider, Lon S / Seeley, William W / Smith, Amanda G / Sonnen, Joshua A / Spina, Salvatore / Stern, Robert A / Swerdlow, Russell H / Tanzi, Rudolph E / Thornton-Wells, Tricia A / Trojanowski, John Q / Troncoso, Juan C / Van Deerlin, Vivianna M / Van Eldik, Linda J / Vinters, Harry V / Vonsattel, Jean Paul / Weintraub, Sandra / Welsh-Bohmer, Kathleen A / Wilhelmsen, Kirk C / Williamson, Jennifer / Wingo, Thomas S / Woltjer, Randall L / Wright, Clinton B / Yu, Chang-En / Yu, Lei / Garzia, Fabienne / Golamaully, Feroze / Septier, Gislain / Engelborghs, Sebastien / Vandenberghe, Rik / De Deyn, Peter P / Fernadez, Carmen Muñoz / Benito, Yoland Aladro / Thonberg, Hakan / Forsell, Charlotte / Lilius, Lena / Kinhult-Stählbom, Anne / Kilander, Lena / Brundin, RoseMarie / Concari, Letizia / Helisalmi, Seppo / Koivisto, Anne Maria / Haapasalo, Annakaisa / Dermecourt, Vincent / Fievet, Nathalie / Hanon, Olivier / Dufouil, Carole / Brice, Alexis / Ritchie, Karen / Dubois, Bruno / Himali, Jayanadra J / Keene, C Dirk / Tschanz, JoAnn / Fitzpatrick, Annette L / Kukull, Walter A / Norton, Maria / Aspelund, Thor / Larson, Eric B / Munger, Ron / Rotter, Jerome I / Lipton, Richard B / Bullido, María J / Hofman, Albert / Montine, Thomas J / Coto, Eliecer / Boerwinkle, Eric / Petersen, Ronald C / Alvarez, Victoria / Rivadeneira, Fernando / Reiman, Eric M / Gallo, Maura / O'Donnell, Christopher J / Reisch, Joan S / Bruni, Amalia Cecilia / Royall, Donald R / Dichgans, Martin / Sano, Mary / Galimberti, Daniela / St George-Hyslop, Peter / Scarpini, Elio / Tsuang, Debby W / Mancuso, Michelangelo / Bonuccelli, Ubaldo / Winslow, Ashley R / Daniele, Antonio / Wu, Chuang-Kuo / Peters, Oliver / Nacmias, Benedetta / Riemenschneider, Matthias / Heun, Reinhard / Brayne, Carol / Rubinsztein, David C / Bras, Jose / Guerreiro, Rita / Al-Chalabi, Ammar / Shaw, Christopher E / Collinge, John / Mann, David / Tsolaki, Magda / Clarimón, Jordi / Sussams, Rebecca / Lovestone, Simon / O'Donovan, Michael C / Owen, Michael J / Behrens, Timothy W / Mead, Simon / Goate, Alison M / Uitterlinden, Andre G / Holmes, Clive / Cruchaga, Carlos / Ingelsson, Martin / Bennett, David A / Powell, John / Golde, Todd E / Graff, Caroline / De Jager, Philip L / Morgan, Kevin / Ertekin-Taner, Nilufer / Combarros, Onofre / Psaty, Bruce M / Passmore, Peter / Younkin, Steven G / Berr, Claudine / Gudnason, Vilmundur / Rujescu, Dan / Dickson, Dennis W / Dartigues, Jean-François / DeStefano, Anita L / Ortega-Cubero, Sara / Hakonarson, Hakon / Campion, Dominique / Boada, Merce / Kauwe, John Keoni / Farrer, Lindsay A / Van Broeckhoven, Christine / Ikram, M Arfan / Jones, Lesley / Haines, Jonathan L / Tzourio, Christophe / Launer, Lenore J / Escott-Price, Valentina / Mayeux, Richard / Deleuze, Jean-François / Amin, Najaf / Holmans, Peter A / Pericak-Vance, Margaret A / Amouyel, Philippe / van Duijn, Cornelia M / Ramirez, Alfredo / Wang, Li-San / Lambert, Jean-Charles / Seshadri, Sudha / Williams, Julie / Schellenberg, Gerard D

Nature genetics

2017 Volume 49, Issue 9, Page(s) 1373–1384

Abstract: We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × ... ...

Abstract	We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Alzheimer Disease/genetics ; Amino Acid Sequence ; Case-Control Studies ; Exome/genetics ; Gene Expression Profiling ; Gene Frequency ; Genetic Predisposition to Disease/genetics ; Genotype ; Humans ; Immunity, Innate/genetics ; Linkage Disequilibrium ; Membrane Glycoproteins/genetics ; Microglia/metabolism ; Odds Ratio ; Phospholipase C gamma/genetics ; Polymorphism, Single Nucleotide ; Protein Interaction Maps/genetics ; Receptors, Immunologic/genetics ; Sequence Homology, Amino Acid
Chemical Substances	ABI3 protein, human ; Adaptor Proteins, Signal Transducing ; Membrane Glycoproteins ; Receptors, Immunologic ; TREM2 protein, human ; Phospholipase C gamma (EC 3.1.4.3)
Language	English
Publishing date	2017-07-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.3916
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma

Mauger, Florence / Dulary, Cécile / Daviaud, Christian / Deleuze, Jean-François / Tost, Jorg

Analytical and bioanalytical chemistry

Volume v. 407,, Issue no. 2

Abstract	Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics, and prediction and monitoring of treatment response, but its amount is usually limited. Therefore, the choice of methods to extract and characterize ccfDNA is crucial. In the current study, we performed the most comprehensive comparison of methods for ccfDNA extraction (11 methods), quantification (3 methods), and estimation of the integrity index (2 methods) from small quantities of different kinds of plasma. The QIAamp® Circulating Nucleic Acid Kit and the Norgen Plasma/Serum Circulating DNA Purification Mini Kit showed the best accuracy and reproducibility, but the Norgen kit allowed to extract a higher amount of ccfDNA. This workflow provides a reliable protocol for the multiple applications of ccfDNA in biomedicine.
Keywords	blood serum ; diagnostic techniques ; monitoring ; DNA ; prediction ; medicine
Language	English
Document type	Article
ISSN	1618-2642
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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Article ; Online: DLK1/DIO3 locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis.

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Article ; Online: Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma.

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Article ; Online: White Blood Cell BRCA1 Promoter Methylation Status and Ovarian Cancer Risk.

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Article ; Online: Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.

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Article: Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma

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