Article
Cell Biology
Shengchao Xu, Chengke Luo, Dikang Chen, Lu Tang, Ling Chen, Zhixiong Liu
Summary: A novel TTFields system (CL-301A) was developed and demonstrated to effectively suppress GBM cell proliferation and induce cell apoptosis. Proteomic and transcriptomic analyses revealed that TTFields mainly affected nuclear proteins and disrupted cell mitosis-related events. Inhibition of autophagy enhanced the anti-GBM activity of TTFields, and CDK2-AS1 might be a target of TTFields in mediating cell cycle arrest.
CELL DEATH & DISEASE
(2022)
Article
Genetics & Heredity
Kazuyoshi Ishigaki, Saori Sakaue, Chikashi Terao, Yang Luo, Kyuto Sonehara, Kensuke Yamaguchi, Tiffany Amariuta, Chun Lai Too, Vincent A. Laufer, Ian C. Scott, Sebastien Viatte, Meiko Takahashi, Koichiro Ohmura, Akira Murasawa, Motomu Hashimoto, Hiromu Ito, Mohammed Hammoudeh, Samar Al Emadi, Basel K. Masri, Hussein Halabi, Humeira Badsha, Imad W. Uthman, Xin Wu, Li Lin, Ting Li, Darren Plant, Anne Barton, Gisela Orozco, Suzanne M. M. Verstappen, John Bowes, Alexander J. MacGregor, Suguru Honda, Masaru Koido, Kohei Tomizuka, Yoichiro Kamatani, Hiroaki Tanaka, Eiichi Tanaka, Akari Suzuki, Yuichi Maeda, Kenichi Yamamoto, Satoru Miyawaki, Gang Xie, Jinyi Zhang, Christopher Amos, Edward Keystone, Gertjan Wolbink, Irene Van der Horst-Bruinsma, Jing Cui, Katherine P. Liao, Robert J. Carroll, Hye-Soon Lee, So-Young Bang, Katherine A. Siminovitch, Niek de Vries, Lars Alfredsson, Solbritt Rantapaa-Dahlqvist, Elizabeth W. Karlson, Sang-Cheol Bae, Robert P. Kimberly, Jeffrey C. Edberg, Xavier Mariette, Tom Huizinga, Philippe Dieude, Matthias Schneider, Martin Kerick, Joshua C. Denny, Koichi Matsuda, Keitaro Matsuo, Tsuneyo Mimori, Fumihiko Matsuda, Keishi Fujio, Yoshiya Tanaka, Atsushi Kumanogoh, Matthew Traylor, Cathryn M. Lewis, Stephen Eyre, Huji Xu, Richa Saxena, Thurayya Arayssi, Yuta Kochi, Katsunori Ikari, Masayoshi Harigai, Peter K. Gregersen, Kazuhiko Yamamoto, S. Louis Bridges, Leonid Padyukov, Javier Martin, Lars Klareskog, Yukinori Okada, Soumya Raychaudhuri
Summary: This study conducted multi-ancestry genome-wide association analyses and identified 124 risk loci for rheumatoid arthritis, of which 34 are novel. The fine-mapping analysis revealed potential causal variants and improved the genetic predictability of rheumatoid arthritis.
Article
Multidisciplinary Sciences
Matteo D'Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Angelo D. Arias, Timothy D. Arthur, Paola Benaglio, W. Travis Berggren, Victor Borja, Juan Carlos Izpisua Belmonte, Megan Cook, Matteo D'Antonio, Agnieszka D'Antonio-Chronowska, Christopher DeBoever, Kenneth E. Diffenderfer, Margaret K. R. Donovan, KathyJean Farnam, Kelly A. Frazer, Kyohei Fujita, Melvin Garcia, Olivier Harismendy, Benjamin A. Henson, David Jakubosky, Kristen Jepsen, He Li, Hiroko Matsui, Naoki Nariai, Jennifer P. Nguyen, Daniel T. O'Connor, Jonathan Okubo, Athanasia D. Panopoulos, Fengwen Rao, Joaquin Reyna, Bianca Salgado, Erin N. Smith, Josh Sohmer, Shawn Yost, William W. Young Greenwald
Summary: Through an eQTL analysis on 966 RNA-seq cardiac samples, the study identifies 2,578 eQTLs associated with specific developmental stages, tissues, and/or cell types. Colocalization analysis between eQTLs and GWAS signals identifies potential causal variants in 210 GWAS loci. The study highlights the impact of cardiac GWAS variants on traits and diseases in a developmental stage-, tissue-, and/or cell type-specific manner.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Matteo P. D'Antonio, Jennifer P. D. Nguyen, Timothy D. Arthur, Hiroko A. Matsui, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer
Summary: This study identifies 2,578 eQTLs associated with specific developmental stages, tissues, and cell types using spatiotemporal information of 966 RNA-seq cardiac samples. The colocalization between eQTLs and GWAS signals reveals the impact of genetic variants on cardiac traits and diseases. These findings shed light on the specific effects of cardiac GWAS variants on developmental stages, tissues, and cell types.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Matteo D'Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer
Summary: The study focuses on identifying the causal variants and genes related to thousands of cardiac genome-wide association study (GWAS) signals. By analyzing the spatiotemporal information of 966 RNA-seq cardiac samples, the researchers detected expression quantitative trait loci (eQTLs) considering both eGenes and eIsoforms. They found eQTLs associated with specific developmental stages, tissues, and/or cell types. Additionally, the colocalization between eQTL and GWAS signals revealed potential causal variants in different cardiac traits.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Matteo D'Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer
Summary: The study identifies genetic variants and gene expression associations specific to developmental stage, organ, tissue, and cell type in cardiac tissues, shedding light on the mechanisms underlying cardiac traits and diseases. These findings suggest a stage-, tissue-, and/or cell type-specific fashion for the impact of genetic variants on cardiac traits and disease.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Jian-Qing Lin, Jun Yu, Li Sun, Sheng-Guo Fang
Summary: The genetic and epigenetic mechanisms underlying sex maintenance in adult Chinese alligators were investigated in this study, identifying specific genes and pathways involved in male and female sex maintenance and gonadal development. Differences in gene expression and DNA methylation levels were observed between male and female gonads, with hypermethylation in gene bodies enhancing the expression of male-biased genes in the testis. These findings provide insights into the conservation of this endangered species.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Omar Hahad, Andreas Daiber, Matthias Michal, Marin Kuntic, Klaus Lieb, Manfred Beutel, Thomas Muenzel
Summary: Despite efforts to combat smoking, it remains a leading cause of morbidity and mortality globally. There is strong evidence linking smoking to increased risk of neuropsychiatric diseases, indicating the importance of addressing this relationship in public health policies and measures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Evolutionary Biology
Cecilia Zumajo-Cardona, Barbara A. Ambrose
Summary: This study analyzed the transcriptome of two Ephedra species with different seed morphologies, revealing differentially expressed genes involved in seed development. The results also supported the hypothesis that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. The study highlights the importance of studying less explored species like gymnosperms in understanding plant evolution.
Article
Agricultural Engineering
Ting Xue, Xuehai Zheng, Duo Chen, Tianyu Zhang, Youqiang Chen, Quanlin Zhong, Baibi Chen, Baoyin Li
Summary: In this study, we investigated the biosynthesis of terpenoids in different stages of Sapindus mukorossi fruit growth using metabolomics and transcriptomics. The results showed that mukurozioside and pyishiauoside of sesquiterpenoids were significantly upregulated in mature fruit, indicating their importance in determining the terpenoid content. Additionally, we identified differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs. This research contributes to our understanding of the molecular mechanisms and regulatory networks involved in terpenoid biosynthesis in S. mukorossi.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Review
Virology
Brittany Bodnar, Kena Patel, Wenzhe Ho, Jin Jun Luo, Wenhui Hu
Summary: Research indicates that Neuro-SARS2 may worsen the severity and mortality of COVID-19. Understanding the neuropathogenesis and cellular mechanisms of Neuro-SARS2 is crucial for developing effective strategies. While progress has been made, there is still much to learn about the neuroinvasive routes of the virus and the mechanisms underlying disease progression.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Plant Sciences
Min Wang, Yupeng Wang, Xiaohui Wang, Guangwei Wei, Huiyi Yang, Xi Yang, Tinghai Shen, Huijie Qu, Sheng Fang, Ziming Wu
Summary: This study identified the high nitrogen use efficiency (NUE) black sesame variety 17-156 and analyzed its underlying physiological and molecular mechanisms. The results showed that 17-156 possesses a sophisticated nitrogen metabolizing machinery to uptake and assimilate higher quantities of inorganic nitrogen, simultaneously improving carbon metabolism and growth. Many important genes were up-regulated in 17-156 under high nitrogen condition. Additionally, 38 potential candidate genes were identified for future studies to improve sesame's NUE. These findings provide valuable resources for understanding the regulatory network of nitrogen metabolism and developing sesame cultivars with improved NUE.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Biotechnology & Applied Microbiology
Nguyen Hoai Nguyen, Benny Jian Rong Sng, Hock Chuan Yeo, In-Cheol Jang
Summary: The study revealed that Brassicaceae vegetables exhibit common signs of shade avoidance syndrome under shade, while also showing distinct responses to shade based on specific gene expression patterns. This finding provides valuable information for developing new shade-tolerant cultivars suitable for high-density indoor farms.
Article
Biochemistry & Molecular Biology
Javier Ib, Lalla Hasna Zinelabidine, Rafael Torres-Perez, Jerome Grimplet, Elisa Baroja, Sergio Ibanez, Pablo Carbonell-Bejerano, Jose Miguel Martinez-Zapater, Javier Ibanez, Javier Tello
Summary: The study revealed that grape yield components are determined by complex polygenic factors, with certain SNPs showing additive effects on the phenotype. This suggests that superior grape cultivars with optimized fruit production can potentially be generated by pyramiding advantageous alleles from different genetic loci.
Article
Food Science & Technology
Yanzi Wang, Honghua Kang, Mengyi Jin, Guoliang Wang, Weifang Ma, Zhen Liu, Yuhua Xue, Cheng Li
Summary: A stable and reliable model of corneal bee sting injury was successfully established, revealing the pathogenesis and therapeutic targets. Hub genes identified in the study are expected to serve as biomarkers and therapeutic targets for the diagnosis and treatment of corneal bee sting.
Article
Psychology, Clinical
Unyoung Chavez-Baldini, Dorien H. Nieman, Amos Keestra, Anja Lok, Roel J. T. Mocking, Pelle de Koning, Valeria V. Krzhizhanovskaya, Claudi L. H. Bockting, Geeske van Rooijen, Dirk J. A. Smit, Arjen L. Sutterland, Karin J. H. Verweij, Guido van Wingen, Johanna T. W. Wigman, Nienke C. Vulink, Damiaan Denys
Summary: Cognitive deficits and psychopathology have independent but related dimensions, and interact in a transdiagnostic manner. Depressive and anxiety symptoms, verbal memory, and visual attention are especially relevant in this network. Future research should take a transdiagnostic approach, focusing on symptom-specific interactions with cognitive domains.
PSYCHOLOGICAL MEDICINE
(2023)
Article
Neurosciences
Helena Voetterl, Guido van Wingen, Giorgia Michelini, Kristi R. Griffiths, Evian Gordon, Roger DeBeus, Mayuresh S. Korgaonkar, Sandra K. Loo, Donna Palmer, Rien Breteler, Damiaan Denys, L. Eugene Arnold, Paul du Jour, Rosalinde van Ruth, Jeanine Jansen, Hanneke van Dijk, Martijn Arns
Summary: This study develops a clinically interpretable and actionable biomarker based on resting-state electroencephalography, which can stratify patients with attention-deficit/hyperactivity disorder to their individual best treatment, thereby increasing remission rates.
BIOLOGICAL PSYCHIATRY-COGNITIVE NEUROSCIENCE AND NEUROIMAGING
(2023)
Article
Psychiatry
Borwin Bandelow, Christer Allgulander, David S. Baldwin, Daniel Lucas da Conceicao Costa, Damiaan Denys, Nesrin Dilbaz, Katharina Domschke, Eric Hollander, Siegfried Kasper, Hans-Juergen Moeller, Elias Eriksson, Naomi A. Fineberg, Josef Haettenschwiler, Hisanobu Kaiya, Tatiana Karavaeva, Martin A. Katzman, Yong-Ku Kim, Takeshi Inoue, Leslie Lim, Vasilios Masdrakis, Jose M. Menchon, Euripedes C. Miguel, Antonio E. Nardi, Stefano Pallanti, Giampaolo Perna, Dan Rujescu, Vladan Starcevic, Dan J. Stein, Shih-Jen Tsai, Michael Van Ameringen, Anna Vasileva, Zhen Wang, Joseph Zohar
Summary: According to the guideline by the World Federation of Societies of Biological Psychiatry, OCD and PTSD can be effectively treated with medications and CBT. SSRIs and CBT are first-line treatments for OCD, while SSRIs and venlafaxine are first-line treatments for PTSD.
WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY
(2023)
Review
Clinical Neurology
Amanda M. Legemaat, Marcella A. S. Haagedoorn, Huibert Burger, Damiaan Denys, Claudi L. Bockting, Gert J. Geurtsen
Summary: This study aimed to assess the proportion of Major Depressive Disorder (MDD) patients with demonstrated valid performance and determine their cognitive functioning. The analysis showed that around 94% of MDD patients had valid neuropsychological test performance in studies using Performance Validity Tests (PVT's). However, there is limited information regarding the cognitive functioning of these patients.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Review
Clinical Neurology
S. E. Cohen, J. B. Zantvoord, B. N. Wezenberg, J. G. Daams, C. L. H. Bockting, D. Denys, G. A. van Wingen
Summary: This study assessed the accuracy of electroencephalography (EEG) in predicting treatment response in major depressive disorder. The results showed that EEG can accurately predict the response to antidepressant treatment, but further validation studies are needed to develop a clinical tool for guiding interventions in MDD.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Review
Neurosciences
Vera Korenblik, Marlies E. Brouwer, Aniko Korosi, Damiaan Denys, Claudi L. H. Bockting, Stanley Brul, Anja Lok
Summary: The microbiota-gut-brain axis (MGBA) is the bidirectional communication between the brain and the gut microbiota, and recent research has linked it to health and disease. This study focuses on understanding the impact of neuromodulation on the gut microbiota, investigating the MGBA from the brain to microbiota. The findings suggest that neuromodulation interventions are associated with moderate changes in the gut microbiome.
Article
Psychiatry
Bram W. C. Storosum, Taina Mattila, Tamar D. Wohlfarth, Christine C. Gispen-de Wied, Kit C. B. Roes, Wim van den Brink, Lieuwe de Haan, Damiaan A. J. P. Denys, Jasper B. Zantvoord
Summary: This study aimed to investigate whether gender and menopausal status have an impact on the response to antipsychotic medication in patients with schizophrenia. The results showed that women had a greater reduction in symptoms compared to men, indicating a higher response to treatment in females.
PSYCHIATRY RESEARCH
(2023)
Article
Neurosciences
Dirk J. A. Smit, Melissa Bakker, Abdel Abdellaoui, Alexander E. Hoetink, Nienke Vulink, Damiaan Denys
Summary: In this study, the genetic etiology of misophonia was investigated, revealing significant correlations between this symptom and tinnitus, major depression disorder, post-traumatic stress disorder, and generalized anxiety disorder, as well as personality traits consistent with anxiety and PTSD.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Psychiatry
Bram W. C. Storosum, Cedrine Steinz, Sem E. E. Cohen, Taina Mattila, Wim van den Brink, Kit Roes, Lieuwe de Haan, Damiaan A. J. P. Denys, Jasper B. B. Zantvoord
Summary: This study analyzed the data of 3880 patients with schizophrenia and found that ethnicity does not moderate the response to antipsychotic medication.
Editorial Material
Genetics & Heredity
Jackson G. Thorp, Zachary F. Gerring, Eske M. Derks
Summary: Identifying genetic variants associated with binge-eating disorder (BED) risk scores using machine learning provides important insights into its etiology and potential intervention targets. This study highlights the pathological role of heme metabolism in BED, overcoming the limitations of under-reporting clinical diagnoses.
Article
Psychiatry
Monique Kammeraat, Geeske van Rooijen, Lisette Kuijper, Julian D. Kiverstein, Damiaan A. J. P. Denys
Summary: Based on the study, the social demographic and psychiatric profiles of patients who requested and received euthanasia and assisted suicide (EAS) were found to be similar. Most of the patients requesting EAS were single females, living independently with a comorbid diagnosis of depression and a history of psychiatric treatment. Among the small group of patients who received EAS, the majority were also single women with depressive disorder. A subgroup of patients with somatic disorders, anxiety disorders, obsessive-compulsive disorders, and neurocognitive disorders were over-represented in the group of patients receiving EAS. Many patients who withdrew their requests for EAS benefited from discussions with end of life experts at EE. Health professionals can make a difference to this vulnerable patient group if they receive training on discussing end of life.
Article
Biochemistry & Molecular Biology
Bo Wang, Shahab Razavi, Eric R. Gamazon
Summary: Deep Mutational Scanning (DMS) allows for the measurement of mutational effects on protein properties with high resolution. In this study, deep learning is applied to model the mutational effects of the Alzheimer's Disease associated peptide A beta 42 on aggregation-related biochemical traits. Neural network architectures such as Convolutional Neural Networks and Recurrent Neural Networks are found to be effective models, even with limited data. The study demonstrates the potential of neural network derived sequence-phenotype mapping in protein engineering and therapeutic design.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Cell Biology
Ying Wang, Shinichi Namba, Esteban Lopera, Sini Kerminen, Kristin Tsuo, Kristi Lall, Masahiro Kanai, Wei Zhou, Kuan-Han Wu, Marie-Julie Fave, Laxmi Bhatta, Philip Awadalla, Ben Brumpton, Patrick Deelen, Kristian Hveem, Valeria Lo Faro, Reedik Magi, Yoshinori Murakami, Serena Sanna, Jordan W. Smoller, Jasmina Uzunovic, Cristen Willer, Eric R. Gamazon, Nancy J. Cox, Ida Surakka, Yukinori Okada, Alicia R. Martin, Jibril Hirbo
Summary: This study utilized data from GBMI to explore methodological considerations and performance of PRS for 14 disease endpoints across global populations. The study provides lessons for PRS construction, evaluation, and interpretation and highlights the importance of PRS in the biobank-scale genomics era.
Article
Biochemical Research Methods
Wanying Zhu, Hung-Hsin Chen, Alexander S. Petty, Lauren E. Petty, Hannah G. Polikowsky, Eric R. Gamazon, Jennifer E. Below, Heather M. Highland
Summary: Combining and handling imputation quality and missing variants in multiple large VCF files in genomic data is challenging. To address this, we developed IMMerge, a Python-based tool that utilizes multiprocessing to reduce running time, and correctly combines imputation quality scores with Fisher's z transformation.
Article
Philosophy
Maarten van Westen, Erik Rietveld, Annemarie van Hout, Damiaan Denys
Summary: Despite technological innovations, clinical expertise remains the cornerstone of psychiatry. Ethnography is a method that can capture the subjective and situation-specific nature of clinical expertise. The study aims to explore the role of clinical expertise in deep brain stimulation optimization for obsessive-compulsive disorder (OCD), and the findings highlight the mutually constitutive relationship between patterns of clinical practice and particular situations.
PHENOMENOLOGY AND THE COGNITIVE SCIENCES
(2023)