Article
Multidisciplinary Sciences
Ming Zhou, Ceyda Coruh, Guanghui Xu, Laura M. Martins, Clara Bourbousse, Alice Lambolez, Julie A. Law
Summary: This study reveals that CLASSY proteins regulate DNA methylation at specific loci in the Arabidopsis genome and control tissue-specific methylation patterns. The lack of individual CLASSY proteins can lead to changes in the epigenetic landscape between tissues, contributing to epigenetic diversity during plant development.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Rongrong Zhao, Huihui Shi, Jiajun Yin, Zhen Sun, Yahui Xu
Summary: The study revealed that the methylation levels of the SSTR4 gene promoter were significantly lower in alcohol-dependent individuals compared to healthy controls, and there was a weak to moderate correlation between methylation levels and alcohol dependence behaviors. This suggests that SSTR4 may play a role in the development of alcohol dependence.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Endika Haro, Florence Petit, Charmaine U. Pira, Conor D. Spady, Sara Lucas-Toca, Lauren Yorozuya, Austin L. Gray, Fabienne Escande, Anne-Sophie Jourdain, Andy Nguyen, Florence Fellmann, Jean-Marc Good, Christine Francannet, Sylvie Manouvrier-Hanu, Marian A. Ros, Kerby C. Oberg
Summary: Nail-patella syndrome (NPS) is characterized by various symptoms including nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma, and can be caused by haploinsufficiency of LMX1B. However, not all patients with NPS have pathogenic mutations in LMX1B. The study demonstrates that loss-of-function variations in upstream enhancer sequences are responsible for a limb specific form of human NPS.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Guangshan Yao, Xinfeng Bai, Bingxin Zhang, Lu Wang, Songbiao Chen, Zonghua Wang
Summary: This study constructed a cell factory based on a marine-derived Aspergillus terreus strain to overproduce the secondary metabolite terrein. By manipulating transcription factors and global regulator genes, the production of terrein was significantly improved. This research provides an efficient strategy for large-scale production of terrein or other secondary metabolites in marine-derived filamentous fungi.
MICROBIAL CELL FACTORIES
(2022)
Article
Plant Sciences
Charles Ampomah-Dwamena, Sumathi Tomes, Amali H. Thrimawithana, Caitlin Elborough, Nitisha Bhargava, Ria Rebstock, Paul Sutherland, Hilary Ireland, Andrew C. Allan, Richard V. Espley
Summary: This study investigates the transcriptional regulation of the carotenoid metabolic pathway in apple. The authors overexpressed a key biosynthetic gene and found that it increased carotenoid content in transgenic fruit. They also discovered that the expression of other carotenoid pathway genes was elevated, suggesting a feed-forward regulation of carotenogenesis. Transcriptome profiling identified several transcription factors that were co-expressed with carotenoid pathway genes. Overall, this study sheds new light on plant carotenogenesis and provides insights into the transcriptional regulation of apple carotenoid biosynthesis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Prakhar Bansal, Darcy T. Ahern, Yuvabharath Kondaveeti, Catherine W. Qiu, Stefan F. Pinter
Summary: Female human pluripotent stem cells (hPSCs) undergo progressive erosion of inactive X chromosome, leading to reactivation of silenced genes. Integrated analysis of DNA methylation, chromatin accessibility, and gene expression identified key regulatory elements and traced the trajectory of X chromosome erosion. Surprisingly, features of naive pluripotency emerge from the altered regulatory landscape, suggesting a potential link to X dosage in human embryonic development.
Article
Biochemistry & Molecular Biology
Cheryl L. Smith, Andrey Poleshko, Jonathan A. Epstein
Summary: Nuclear architecture influences gene regulation and cell identity by controlling the three-dimensional organization of genes and their distal regulatory sequences. KODs, a novel type of nuclear peripheral chromatin domain enriched for tissue-specific transcriptional enhancers, show limited Lamin B interaction and are characterized by low gene expression and enhancers in an inactive or poised state. These KODs may play a role in regulating spatiotemporal gene expression programs during differentiation and development.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Wuchen Yin, Xianhang Wang, Hui Liu, Ya Wang, Steve van Nocker, Mingxing Tu, Jinghao Fang, Junqiang Guo, Zhi Li, Xiping Wang
Summary: Transgenic expression of the WRKY transcription factor gene VqWRKY31 from the PM-resistant species Vitis quinquangularis enhanced resistance to powdery mildew in V. vinifera by activating salicylic acid defense signaling and promoting the synthesis of specific disease resistance-related metabolites. These findings have important implications for molecular breeding strategies to produce PM-resistant grapevine germplasm.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bryan A. Ramirez-Corona, Stephanie Fruth, Oluchi Ofoegbu, Zeba Wunderlich
Summary: The study found that the mode of expression divergence varies between conditions within the Drosophila fat body. Trans-acting effects dominate in response to Gram-negative infection, while cis-acting effects dominate in Gram-positive and preinfection conditions. Before infection, compensatory effects in the fat body due to metabolic activity lead to changes in cis and trans that counteract each other.
Article
Forestry
Xiaojin Lei, Jiaru Fang, JiaXin Lv, Zhengyang Li, Zhongyuan Liu, Yucheng Wang, Chao Wang, Caiqiu Gao
Summary: ThSCL32 gene is highly induced by salt stress and improves salt tolerance in Tamarix hispida. It enhances ThPHD3 gene expression, possibly through binding to the novel cis-element SBS in the promoter of ThPHD3.
Review
Plant Sciences
Xiaoman Zou, Hongmei Sun
Summary: Plant biological processes are regulated by gene transcriptional regulation, in which transcription factors play a crucial role. DOF (DNA binding with One Finger) is a plant-specific transcription factor family characterized by its single zinc finger structure, and recent studies have shown their vital roles in various biological processes. This article reviews the origin, evolution, protein structure, and functions of DOF members reported in studies to provide directions for future research.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Carolina M. Pusec, Vladimir Ilievski, Adam De Jesus, Zeenat Farooq, Joseph L. Zapater, Nadia Sweis, Hagar Ismail, Md Wasim Khan, Hossein Ardehali, Jose Cordoba-Chacon, Brian T. Layden
Summary: The liver plays a primary role in regulating glucose homeostasis. Glucokinase (GCK) is the main hexokinase (HK) expressed in hepatocytes, which phosphorylates glucose to glucose-6-phosphate (G6P) for further metabolic pathways. HKDC1, a novel hexokinase, has been found to have low basal expression in normal liver but increases during stress states and is associated with liver diseases.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Wenjie Wang, Yuchao Yu, Nancy P. Keller, Pinmei Wang
Summary: Fungal secondary metabolites are both toxic and valuable sources of drugs, regulated by pathway specific transcription factors (PSTFs) in biosynthetic gene clusters (BGCs). The size of BGCs can predict the presence of PSTFs, and the number and relative location of PSTFs can affect their regulation of gene clusters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Immunology
Kazuko Miyazaki, Masaki Miyazaki
Summary: This article discusses the driving factors of cell type-specific gene expression, emphasizing the importance of the interplay between chromatin architectures and TFs in cell fate decisions and cell type-specific functions, as well as the key roles of SEs and Rag1/2 genes in adaptive immunity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Se Eun Jung, Seung Woon Bang, Sung Hwan Kim, Jun Sung Seo, Ho-Bin Yoon, Youn Shic Kim, Ju-Kon Kim
Summary: OsERF83, a member of the AP2/ERF transcription factor family, plays an important role in response to drought stress by enhancing drought tolerance in rice while potentially causing growth retardation. It is predominantly expressed in the vascular tissue of all organs and regulates multiple gene pathways involved in responses to both abiotic and biotic stresses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Adrien Breiman, Nathalie Ruvoen-Clouet, Marie Deleers, Tiffany Beauvais, Nicolas Jouand, Jezabel Rocher, Nicolai Bovin, Nathalie Labarriere, Hanane El Kenz, Jacques Le Pendu
Summary: The study reveals that COVID-19 patients have significantly lower levels of anti-Tn antibodies compared to non-infected individuals, indicating both quantitative and qualitative differences. The anti-Tn antibodies are correlated with the development of specific antiviral response and are also lower in individuals with blood types A and B.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Oncology
Marisa Capitao, Justine Perrin, Sylvain Simon, Sebastien Gouard, Nicolas Chouin, Frank Bruchertseifer, Alfred Morgenstern, Latifa Rbah-Vidal, Michel Cherel, Emmanuel Scotet, Nathalie Labarriere, Yannick Guilloux, Joelle Gaschet
Summary: The study demonstrates that targeting PD-L1 with bismuth-213, an alpha-particle emitter, leads to efficient anti-tumor response, significant tumor growth delay, and improved survival in human melanoma, suggesting that anti-PD-L1 antibodies could be a promising therapeutic option for targeted alpha-particle therapy.
Article
Oncology
Brigitte Dreno, Amir Khammari, Agnes Fortun, Virginie Vignard, Soraya Saiagh, Tiffany Beauvais, Nicolas Jouand, Sylvain Bercegay, Sylvain Simon, Francois Lang, Nathalie Labarriere
Summary: The study demonstrated the feasibility and safety of using Melan-A and MELOE-1 specific T cells for ACT in metastatic melanoma patients, but the clinical efficacy can be further enhanced by selecting highly reactive T cells based on PD-1 and TIGIT co-expression and combining with ICI such as anti-PD-1.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Oncology
Maud Charpentier, Emilie Dupre, Agnes Fortun, Floriane Briand, Mike Maillasson, Emmanuelle Com, Charles Pineau, Nathalie Labarriere, Catherine Rabu, Francois Lang
Summary: The main challenge in cancer immunotherapy is selecting relevant tumor antigens. The study investigates the translation control of MELOE-1 and its role in melanoma cells. It shows that promoting hnRNP-A1 translation in tumor cells enhances MELOE-1 recognition and the efficacy of immunotherapies.
MOLECULAR ONCOLOGY
(2022)
Article
Genetics & Heredity
Sebastien Kury, Frederic Ebstein, Alice Molle, Thomas Besnard, Ming-Kang Lee, Virginie Vignard, Tiphaine Hery, Mathilde Nizon, Grazia M. S. Mancini, Jacques C. Giltay, Benjamin Cogne, Kirsty McWalter, Wallid Deb, Hagar Mor-Shaked, Hong Li, Rhonda E. Schnur, Ingrid M. Wentzensen, Anne-Sophie Denomme-Pichon, Cynthia Fourgeux, Frans W. Verheijen, Eva Faurie, Rachel Schot, Cathy A. Stevens, Daphne J. Smits, Eileen Barr, Ruth Sheffer, Jonathan A. Bernstein, Chandler L. Stimach, Eliana Kovitch, Vandana Shashi, Kelly Schoch, Whitney Smith, Richard H. van Jaarsveld, Anna C. E. Hurst, Kirstin Smith, Evan H. Baugh, Suzanne G. Bohm, Emilie Vyhnalkova, Lukas Ryba, Capucine Delnatte, Juanita Neira, Dominique Bonneau, Annick Toutain, Jill A. Rosenfeld, Severine Audebert-Bellanger, Brigitte Gilbert-Dussardier, Sylvie Odent, Frederic Laumonnier, Seth Berger, Ann C. M. Smith, Franck Bourdeaut, Marc-Henri Stern, Richard Redon, Elke Krueger, Raphael Margueron, Stephane Bezieau, Jeremie Poschmann, Bertrand Isidor
Summary: This study reports on a rare syndromic neurodevelopmental disorder caused by rare germline missense BAP1 variants, and provides evidence that these variants alter chromatin remodeling and transcriptional dysregulation of developmental genes.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Bertrand Isidor, Frederic Ebstein, Anna Hurst, Marie Vincent, Ingrid Bader, Natasha L. Rudy, Benjamin Cogne, Johannes Mayr, Anja Brehm, Caleb Bupp, Kathryn Warren, Carlos A. Bacino, Amanda Gerard, Judith D. Ranells, Kay A. Metcalfe, Yolande van Bever, Yong-Hui Jiang, Bryce A. Mendelssohn, Heidi Cope, Jill A. Rosenfeld, Patrick R. Blackburn, McKinsey L. Goodenberger, Hutton M. Kearney, Joanna Kennedy, Ingrid Scurr, Krzysztof Szczaluba, Rafal Ploski, Anne de Saint Martin, Yves Alembik, Amelie Piton, Ange-Line Bruel, Christel Thauvin-Robinet, Alanna Strong, Karin E. M. Diderich, Dominique Bourgeois, Karin Dahan, Virginie Vignard, Dominique Bonneau, Estelle Colin, Magalie Barth, Caroline Camby, Genevieve Baujat, Ignacio Briceno, Alberto Gomez, Wallid Deb, Solene Conrad, Thomas Besnard, Stephane Bezieau, Elke Krueger, Sebastien Kury, Pawel Stankiewicz
Summary: This study further explores the clinical and molecular phenotypic spectrum of Stankiewicz-Isidor syndrome (STISS). The findings indicate that STISS patients exhibit highly variable clinical features, including developmental delay, intellectual disability, speech delay, cardiac and renal anomalies, and hand abnormalities. Additionally, the study reveals significant remodeling of the mTORC1 and mitophagy pathways in STISS patient cells, with induction of type I interferon-stimulated genes.
GENETICS IN MEDICINE
(2022)
Editorial Material
Immunology
Janin Chandra, Morten Hansen, Nathalie Labarriere, Ilaria Marigo, Fernando Souza-Fonseca-Guimaraes, Lazar Vujanovic, Yoshinobu Koguchi, Nicolas Jacquelot
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Kathleen Ducoin, Romain Oger, Linda Bilonda Mutala, Cecile Deleine, Nicolas Jouand, Juliette Desfrancois, Juliette Podevin, Emilie Duchalais, Jonathan Cruard, Houssem Benlalam, Nathalie Labarriere, Celine Bossard, Anne Jarry, Nadine Gervois-Segain
Summary: In colorectal cancer, the NKG2A(+) CD8(+) T lymphocyte subpopulation shows enrichment in tumors, terminal exhaustion status, co-expression of other immune checkpoints, high functional avidity, and inhibition of anti-tumor reactivity that can be overcome by blocking NKG2A.
Article
Genetics & Heredity
Sebastien Kury, Jinwei Zhang, Thomas Besnard, Alfonso Caro-Llopis, Xue Zeng, Stephanie M. Robert, Sunday S. Josiah, Emre Kiziltug, Anne-Sophie Denomme-Pichon, Benjamin Cogne, Adam J. Kundishora, Le T. Hao, Hong Li, Roger E. Stevenson, Raymond J. Louie, Wallid Deb, Erin Torti, Virginie Vignard, Kirsty McWalter, F. Lucy Raymond, Farrah Rajabi, Emmanuelle Ranza, Detelina Grozeva, Stephanie A. Coury, Xavier Blanc, Elise Brischoux-Boucher, Boris Keren, Katrin Ounap, Karit Reinson, Pilvi Ilves, Ingrid M. Wentzensen, Eileen E. Barr, Solveig Heide Guihard, Perrine Charles, Eleanor G. Seaby, Kristin G. Monaghan, Marlene Rio, Yolande van Bever, Marjon van Slegtenhorst, Wendy K. Chung, Ashley Wilson, Delphine Quinquis, Flora Breheret, Kyle Retterer, Pierre Lindenbaum, Emmanuel Scalais, Lindsay Rhodes, Katrien Stouffs, Elaine M. Pereira, Sara M. Berger, Sarah S. Milla, Ankita B. Jaykumar, Melanie H. Cobb, Shreyas Panchagnula, Phan Q. Duy, Marie Vincent, Sandra Mercier, Brigitte Gilbert-Dussardier, Xavier Le Guillou, Severine Audebert-Bellanger, Sylvie Odent, Sebastien Schmitt, Pierre Boisseau, Dominique Bonneau, Annick Toutain, Estelle Colin, Laurent Pasquier, Richard Redon, Arjan Bouman, Jill A. Rosenfeld, Michael J. Friez, Helena Perez-Pena, Syed Raza Akhtar Rizvi, Shozeb Haider, Stylianos E. Antonarakis, Charles E. Schwartz, Francisco Martinez, Stephane Bezieau, Kristopher T. Kahle, Bertrand Isidor
Summary: This study identified WNK3 gene variants associated with a rare form of X-linked intellectual disability, which showed variable manifestations of epilepsy and structural brain abnormalities. The study also revealed impaired phosphorylation regulation of KCC2 as a possible mechanism underlying the disease.
GENETICS IN MEDICINE
(2022)
Article
Immunology
Pierre Autin, Sophie Deshayes, Juliette Lea, Nicolas Boisgerault, Emilie Dupre, Nathalie Labarriere, Remy Leguevel, Jean-Francois Fonteneau, Christophe Blanquart, Delphine Fradin
Summary: The herbicide DCMU modulates the expression of miRNA in a dose-dependent manner, leading to reduced secretion of cytokines and granzyme B. This decreases the cytotoxic activity of CD8+ T cells against cancer cells.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Quentin Thomas, Marialetizia Motta, Thierry Gautier, Maha S. Zaki, Andrea Ciolfi, Julien Paccaud, Francois Girodon, Odile Boespflug-Tanguy, Thomas Besnard, Jennifer Kerkhof, Haley McConkey, Aymeric Masson, Anne-Sophie Denomme-Pichon, Benjamin Cogne, Eva Trochu, Virginie Vignard, Fatima El It, Lance H. Rodan, Mohammad Ayman Alkhateeb, Rami Abou Jamra, Laurence Duplomb, Emilie Tisserant, Yannis Duffourd, Ange-Line Bruel, Adam Jackson, Siddharth Banka, Meriel McEntagart, Anand Saggar, Joseph G. Gleeson, David Sievert, Hyunwoo Bae, Beom Hee Lee, Kisang Kwon, Go Hun Seo, Hane Lee, Anjum Saeed, Nadeem Anjum, Huma Cheema, Salem Alawbathani, Imran Khan, Jorge Pinto-Basto, Joyce Teoh, Jasmine Wong, Umar Bin Mohamad Sahari, Henry Houlden, Kristina Zhelcheska, Melanie Pannetier, Mona A. Awad, Marion Lesieur-Sebellin, Giulia Barcia, Jeanne Amiel, Julian Delanne, Christophe Philippe, Laurence Faivre, Sylvie Odent, Aida Bertoli-Avella, Christel Thauvin, Bekim Sadikovic, Bruno Reversade, Reza Maroofian, Jerome Govin, Marco Tartaglia, Antonio Vitobello
Summary: Through international data sharing, we identified that bi-allelic loss-of-function variants in the TMEM147 gene cause syndromic intellectual disability due to dysfunction in the endoplasmic reticulum and nuclear organization. The affected children display consistent clinical features, including coarse facies, developmental delay, intellectual disability, and behavioral problems. These findings have important implications for research on neurodevelopment and intellectual disabilities.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Meeting Abstract
Radiology, Nuclear Medicine & Medical Imaging
L. Marotte, M. Capitao, C. Deleine, T. Beauvais, G. Cadiou, J. Perrin, M. Cherel, Y. Guilloux, E. Scotet, F. Bruchertseifer, A. Morgenstern, A. Jarry, N. Labarriere, J. Gaschet
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2021)