Article
Multidisciplinary Sciences
Rebecca J. Carlson, Michael D. Leiken, Alina Guna, Nir Hacohen, Paul C. Blainey
Summary: This study used high-throughput imaging technology and genome-wide CRISPR knockout screening to identify regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. The study also found that the ER-localized P5A-type ATPase ATP13A1 is essential for viral sensing and is involved in promoting the localization of MAVS to mitochondrial membranes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Ohad Yogev, Omer Weissbrod, Giorgia Battistoni, Dario Bressan, Adi Naamati, Ilaria Falciatori, Ahmet Can Berkyurek, Roni Rasnic, Rhys Izuagbe, Myra Hosmillo, Shaul Ilan, Iris Grossman, Lauren McCormick, Christopher Cole Honeycutt, Timothy Johnston, Matthew Gagne, Daniel C. Douek, Ian Goodfellow, Gregory James Hannon, Yaniv Erlich
Summary: A genome-wide screen identified hyper-potent RNAi candidates against SARS-CoV-2, which were further validated in vitro and in vivo. These siRNAs exhibited strong activity against multiple variants of concern and provided broad protection. Intranasal administration of the siRNA cocktail effectively attenuated clinical signs and viral measures in a hamster model, highlighting the potential for an additional layer of antiviral prophylaxis.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
Xuejiao Jin, Jie Zhang, Tingting An, Huihui Zhao, Wenhao Fu, Danqi Li, Shenkui Liu, Xiuling Cao, Beidong Liu
Summary: Research reveals that lithium hexafluorophosphate (LiPF6) is more toxic to yeast than lithium chloride or sodium hexafluorophosphate, causing mitochondrial damage, reactive oxygen species accumulation, and ATP content changes leading to cytotoxicity. Genome-wide screening shows oxidative phosphorylation-related gene deletion mutants are specifically hypersensitive to LiPF6, with higher ROS production and reduced ATP levels upon treatment, suggesting their importance in counteracting LiPF6-induced toxicity.
Article
Nanoscience & Nanotechnology
Di Zhang, Guoxun Wang, Xueliang Yu, Tuo Wei, Lukas Farbiak, Lindsay T. Johnson, Alan Mark Taylor, Jiazhu Xu, Yi Hong, Hao Zhu, Daniel J. Siegwart
Summary: Modulating the mechanical properties of tumor cells enhances gene editing and inhibits tumor growth by using dendrimer lipid nanoparticles for PD-L1 gene editing and knocking out FAK.
NATURE NANOTECHNOLOGY
(2022)
Editorial Material
Cell Biology
Giulia Cerrato, Oliver Kepp, Allan Sauvat, Guido Kroemer
Summary: Oleate blocks conventional protein secretion and induces the local enrichment of LC3 at the trans-Golgi network, independent of the recruitment of LC3 to the Golgi apparatus.
Article
Cell Biology
Wei Wang, Yuxuan Zheng, Shuhui Sun, Wei Li, Moshi Song, Qianzhao Ji, Zeming Wu, Zunpeng Liu, Yanling Fan, Feifei Liu, Jingyi Li, Concepcion Rodriguez Esteban, Si Wang, Qi Zhou, Juan Carlos Izpisua Belmonte, Weiqi Zhang, Jing Qu, Fuchou Tang, Guang-Hui Liu
Summary: Understanding the genetic and epigenetic factors of cellular senescence is crucial for developing interventions to slow aging. CRISPR-Cas9-based screens identified genes like KAT7 that alleviate senescence in accelerated aging models, and lentiviral vectors encoding Cas9/sg-Kat7 were effective in alleviating cellular aging and extending lifespan.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Oncology
Mingrui Du, Jintao Gu, Chenlin Liu, Nannan Liu, Zhe Yu, Chengpei Zhou, Wei Heng, Zhengcong Cao, Feilong Wei, Kailong Zhu, Yingwen Wang, Wei Zhang, Xiaochang Xue, Yong Zhang, Jixian Qian
Summary: In this study, Rad18 was identified as a driver of doxorubicin resistance in OS, promoting the activation of the HR pathway. Targeting Rad18 proves to be an effective approach to overcome chemotherapy resistance in OS.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Biophysics
Sayane Shome, Kejue Jia, Sanjeevi Sivasankar, Robert L. Jernigan
Summary: This study focuses on the intermolecular interactions of E-cadherin, using coevolutionary sequence analysis and molecular dynamics simulations to identify known and novel interaction sites. The study reveals the existence of a potential new cis interface at the EC3-EC5 domain in addition to established interaction sites, and identifies specific mutations that impair cell adhesion within E-cadherin assemblies.
BIOPHYSICAL JOURNAL
(2023)
Article
Microbiology
Yu Wang, Han Fu, Xiao-Jie Shi, Guo-Ping Zhao, Liang-Dong Lyu
Summary: The antibacterial activity of rifamycins relies on the inhibition of transcription by directly binding to bacterial DNA-dependent RNA polymerase (RNAP). However, this killing efficacy is limited in most gram-negative bacteria. In this study, we identified the cellular functions that counteract rifamycin-mediated killing in Escherichia coli, a gram-negative model organism, and found that the beta-barrel assembly machinery plays a crucial role in restricting rifampicin from entering the cell. Additionally, cellular functions such as iron acquisition, DNA repair, aerobic respiration, and carbon metabolism strongly influenced the killing efficacy of rifampicin. Maintenance of DNA replication and transcription-coupled nucleotide excision repair protected E. coli cells against rifampicin killing, while sustained aerobic respiration and carbon catabolism diminished rifampicin's killing efficacy.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Masaki Kimura, Takuma Iguchi, Kentaro Iwasawa, Andrew Dunn, Wendy L. Thompson, Yosuke Yoneyama, Praneet Chaturvedi, Aaron M. Zone, Michelle Wintzinger, Matti Quattorcelli, Miki Watanabe-Chailland, Gaohui Zhu, Masanobu Fujimoto, Meenasri Kumbaji, Asuka Kodaka, Yevgeniy Gindin, Chuhan Chung, Robert P. Myers, G. Mani Subramanian, Vivian Hwa, Takanori Takebe
Summary: The study found that the gene GCKR-rs1260326 has different effects on the disease under different metabolic states, providing new insights for future therapeutic approaches for diabetic NASH.
Article
Biochemistry & Molecular Biology
Michael T. J. Hague, J. Dylan Shropshire, Chelsey N. Caldwell, John P. Statz, Kimberly A. Stanek, William R. Conner, Brandon S. Cooper
Summary: This study provides an unexpectedly simple explanation for the prevalence of the Wolbachia endosymbiont in Drosophila melanogaster. It shows that lowering temperatures decrease cellular abundance of the Wolbachia during a key stage of the host's reproductive process, resulting in temperature-dependent variation in maternal transmission. This finding plausibly explains the variation in Wolbachia frequencies observed on different continents. Genomic analysis identifies specific alleles that underlie the thermal sensitivity of cellular Wolbachia abundance and covary with temperature globally. The study highlights the importance of temperature as a key determinant of Wolbachia spread and equilibrium frequencies.
Article
Multidisciplinary Sciences
Yicun Wang, Jinhui Wu, Hui Chen, Yang Yang, Chengwu Xiao, Xiaoming Yi, Changjie Shi, Ke Zhong, Haowei He, Yaoming Li, Zhenjie Wu, Guangxin Zhou, Qiu Rao, Xiaoxia Wang, Xiaodie Zhou, Gwen Lomberk, Bing Liu, Jianning Zhao, Jingping Ge, Wenquan Zhou, Xiaoyuan Chu, Cheng Chen, Xuhui Zhou, Linhui Wang, Kunliang Guan, Le Qu
Summary: The study identified KLF11 as a negative regulator in sarcoma cancer stem cells, forming a negative feedback loop with YAP/TEAD. Epigenetic silencing of KLF11 in CSCs leads to sustained YAP activation, which is associated with poor prognosis and chemotherapy response in sarcoma patients. Pharmacological activation of KLF11 effectively restored chemotherapy response.
Article
Biochemistry & Molecular Biology
Diego Lucero, Ozan Dikilitas, Michael M. Mendelson, Zahra Aligabi, Promotto Islam, Edward B. Neufeld, Aruna T. Bansal, Lita A. Freeman, Boris Vaisman, Jingrong Tang, Christian A. Combs, Yuesheng Li, Szilard Voros, Iftikhar J. Kullo, Alan T. Remaley
Summary: A novel gene screening method identified transgelin (TAGLN) as a potentially new gene involved in LDL endocytosis. Research found a significant association between TAGLN and human plasma lipids, impacting cholesterol metabolism by influencing LDL uptake.
JOURNAL OF LIPID RESEARCH
(2022)
Article
Chemistry, Medicinal
Jade Young, Neerja Garikipati, Jacob D. Durrant
Summary: BINANA is an algorithm used to identify and characterize receptor/ligand interactions. The algorithm has been updated to be more accessible and can now be used for analysis in web browsers. A web-browser application has been created to allow students and chemical-biology researchers to visualize receptor/ligand complexes and their binding interactions quickly.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Pol Picon-Pages, Monica Bosch-Morato, Laia Subirana, Francisca Rubio-Moscardo, Biuse Guivernau, Hugo Fanlo-Ucar, Melisa Ece Zeylan, Simge Senyuz, Victor Herrera-Fernandez, Ruben Vicente, Jose M. Fernandez-Fernandez, Jordi Garcia-Ojalvo, Attila Gursoy, Ozlem Keskin, Baldomero Oliva, Francesc Posas, Eulalia de Nadal, Francisco J. Munoz
Summary: Alzheimer's disease is caused by misfolded amyloid beta-peptide (Aβ) forming beta-sheets, but there are currently no treatments available to prevent it. Through a genome-wide screen in Saccharomyces cerevisiae, we identified 81 mammalian orthologue genes that enhance Aβ(1-42) toxicity and 157 that provide protection. Further studies revealed that calcium regulation, protein translation, and mitochondrial activity were the main cellular functions affected by Aβ oligomers (oAβ). We focused on SURF4, a protein that regulates the store-operated calcium channel (SOCE), and found that it contributes to oAβ(1-42) neurotoxicity by decreasing SOCE activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Correction
Biotechnology & Applied Microbiology
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Adam P. Butler, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Brandi N. Davis-Dusenbery, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Roland Eils, Kyle Ellrott, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Vincent Ferretti, Paul Flicek, Nuno A. Fonseca, Josep Ll. Gelpi, Gad Getz, Bob Gibson, Robert L. Grossman, Olivier Harismendy, Allison P. Heath, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Barbara Hutter, Carolyn M. Hutter, Daniel Hubschmann, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyung-Lae Kim, Hyunghwan Kim, Jihoon Kim, Youngwook Kim, Kortine Kleinheinz, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Jia Liu, Dimitri Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Naoki Miyoshi, Hardeep K. Nahal-Bose, Hidewaki Nakagawa, Mia Nastic, Steven J. Newhouse, Jonathan Nicholson, Brian D. O'Connor, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B. F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggros, Petar Radovic, Keiran M. Raine, Esther Rheinbay, Mara Rosenberg, Romina Royo, Gunnar Ratsch, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Charles Short, Heidi J. Sofia, Jonathan Spring, Lincoln D. Stein, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, David Torrents, Peter Van Loo, Miguel Vazquez, David Vicente, Jeremiah A. Wala, Zhining Wang, Sebastian M. Waszak, Joachim Weischenfeldt, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, Liming Yang, Denis Yuen, Christina K. Yung, Junjun Zhang, Jan O. Korbel
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xavier Hernandez-Alias, Christopher D. Katanski, Wen Zhang, Mahdi Assari, Christopher P. Watkins, Martin H. Schaefer, Luis Serrano, Tao Pan
Summary: Transfer RNA (tRNA) utilizes its abundance, modification, and aminoacylation properties for translational regulation. By developing a new tRNA analysis pipeline, we discovered correlations among various properties and identified the coordinating role of one common modification in tissue-specific gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Andrea Zanotti, Joao P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Donem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, Matthias J. Feige
Summary: This study reveals a previously unknown function of the human signal peptidase complex (SPC) as a membrane protein quality control factor. The SPC cleaves membrane proteins at hidden cleavage sites when they fail to fold or assemble correctly, contributing to membrane protein homeostasis and cellular fitness.
Article
Cell Biology
Mariam G. Aslanyan, Cenna Doornbos, Gaurav D. Diwan, Zeinab Anvarian, Tina Beyer, Katrin Junger, Sylvia E. C. van Beersum, Robert B. Russell, Marius Ueffing, Alexander Ludwig, Karsten Boldt, Lotte B. Pedersen, Ronald Roepman
Summary: By studying ubiquitination modifications in cells, we have identified the involvement of ESCRT-dependent clathrin-mediated endocytosis vesicles and caveolae components in ciliary function. These findings contribute to a better understanding of the mechanisms underlying cilia biology in health and disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Neurosciences
Michael Maes, Asara Vasupanrajit, Ketsupar Jirakran, Pavit Klomkliew, Prangwalai Chanchaem, Chavit Tunvirachaisakul, Kitiporn Plaimas, Apichat Suratanee, Sunchai Payungporn
Summary: This study found that major depressive disorder is associated with alterations in the gut microbiota. Six microbiome taxa were found to be related to depression phenome, and another microbiome taxa was associated with lowered high-density lipoprotein cholesterol. These findings suggest that the gut microbiota could be a potential target for the treatment of depression and prevention of future episodes.
ACTA NEUROPSYCHIATRICA
(2023)
Article
Cell & Tissue Engineering
Duncan C. Miller, Pawel Lisowski, Carolin Genehr, Erich E. Wanker, Josef Priller, Alessandro Prigione, Sebastian Diecke
Summary: Huntington's disease (HD) is caused by abnormal CAG repeats in the HTT gene, resulting in an elongated poly-Q sequence in HTT. In this study, fibroblasts from a patient with juvenile onset HD were reprogrammed into iPSCs using a non-integrative Sendai virus. The reprogrammed iPSCs expressed pluripotency markers, maintained a normal karyotype, and could differentiate into various cell types. PCR analysis and sequencing confirmed the presence of one normal HTT allele and one with elongated CAG repeats in the HD patient-derived iPSC line, equivalent to >= 180Q.
STEM CELL RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Fabiola De Marchi, Toni Franjkic, Paride Schito, Tommaso Russo, Jerneja Nimac, Anna A. Chami, Angelica Mele, Lea Vidatic, Jasna Kriz, Jean-Pierre Julien, Gordana Apic, Robert B. Russell, Boris Rogelj, Jason R. Cannon, Marco Baralle, Federica Agosta, Silva Hecimovic, Letizia Mazzini, Emanuele Buratti, Ivana Munitic
Summary: Proteinopathy and neuroinflammation are two main features of neurodegenerative diseases with high heterogeneity. This review focuses on ALS and FTD spectrum disorder, highlighting neuroinflammation and immune imbalance as novel therapeutic targets. Dysregulation of TDP-43 is a common mechanism in most ALS and 50% of FTD patients, leading to altered cellular events. Experimental attempts targeting TDP-43 aggregates and inflammation will be discussed.
Article
Infectious Diseases
Tanatorn Intarapanya, Apichat Suratanee, Sittiporn Pattaradilokrat, Kitiporn Plaimas
Summary: COVID-19 is a rapidly spreading respiratory disease, and vaccination is an important measure to control its spread and reduce infections. Different types of vaccines have varying efficacy in preventing and alleviating symptoms. A mathematical model, SVIHR, was developed to assess disease transmission in Thailand considering vaccine efficacy and vaccination rate. Equilibrium points and the basic reproduction number (R-0) were calculated, showing that stability depends on R-0 values. Simulation results and parameter estimates applied to actual data in Thailand were reported. The trade-off between vaccine efficacy and vaccination rate was investigated, highlighting the importance of vaccine efficacy in restricting COVID-19 spread.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Article
Chemistry, Multidisciplinary
Apichat Suratanee, Kitiporn Plaimas
Summary: Through the integration of multiple data sources, we conducted a systematic analysis to reveal genes associated with Autism Spectrum Disorder (ASD). We generated a gene embedding profile and a differential gene expression profile, and utilized the XGBoost classifier to identify potential gene-gene associations and candidate genes. Our analysis identified 10,848 potential gene-gene associations and inferred 125 candidate genes, with DNA Topoisomerase I, ATP Synthase F1 Subunit Gamma, and Neuronal Calcium Sensor 1 being the top candidates. We also assessed the relevance of candidate genes to specific functions and pathways and identified sub-networks within the candidate network. Overall, our analysis contributes to ASD research and facilitates the discovery of new targets for molecularly targeted therapies.
APPLIED SCIENCES-BASEL
(2023)
Article
Horticulture
Tanapon Saelao, Panita Chutimanukul, Apichat Suratanee, Kitiporn Plaimas
Summary: This study examines the diversity of antioxidant capacities among various Thai holy basil cultivars and identifies four distinct groups based on their characteristics. The findings lay the foundation for targeted breeding strategies and informed choices regarding consumption.
Article
Immunology
Maria Gevezova, Yordan Sbirkov, Victoria Sarafian, Kitiporn Plaimas, Apichat Suratanee, Michael Maes
Summary: Through the analysis of large-scale gene expression data from 1355 ASD patients and 1110 controls, abnormalities in transcription factors and immune-inflammatory pathways were found in the brains and peripheral blood of ASD patients. These abnormalities lead to impairments in neurodevelopment and social behaviors, and are associated with neuroinflammation and mitochondrial dysfunction induced by viral infections.
BRAIN, BEHAVIOR, & IMMUNITY - HEALTH
(2023)
Article
Cell Biology
Grace Mercedes Freke, Tiago Martins, Rosalind Jane Davies, Tina Beyer, Marian Seda, Emma Peskett, Naila Haq, Avishek Prasai, Georg Otto, Jeshmi Jeyabalan Srikaran, Victor Hernandez, Gaurav D. Diwan, Robert B. Russell, Marius Ueffing, Martina Huranova, Karsten Boldt, Philip L. Beales, Dagan Jenkins
Summary: Bardet-Biedl syndrome is a ciliopathy that affects multiple tissues. Research suggests that BBS1 plays a crucial role in suppressing the transition from epithelial cells to mesenchymal cells, and dysregulation of epithelial-to-mesenchymal transition genes may be a predisposing feature of BBS.
Article
Computer Science, Artificial Intelligence
Panisa Janyasupab, Apichat Suratanee, Kitiporn Plaimas
Summary: GeneCompete is a powerful web-based tool that revolutionizes the identification of disease-causing genes through the integration of gene expression data from multiple platforms and experiments.
PEERJ COMPUTER SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Philipp Georg, Rosario Astaburuaga-Garcia, Lorenzo Bonaguro, Sophia Brumhard, Laura Michalick, Lena J. Lippert, Tomislav Kostevc, Christiane Gaebel, Maria Schneider, Mathias Streitz, Vadim Demichev, Ioanna Gemuend, Matthias Barone, Pinkus Tober-Lau, Elisa T. Helbig, David Hillus, Lev Petrov, Julia Stein, Hannah-Philine Dey, Daniela Paclik, Christina Iwert, Michael Muelleder, Simran Kaur Aulakh, Sonja Djudjaj, Roman D. Buelow, Henrik E. Mei, Axel R. Schulz, Andreas Thiel, Stefan Hippenstiel, Antoine-Emmanuel Saliba, Roland Eils, Irina Lehmann, Marcus A. Mall, Sebastian Stricker, Jobst Roehmel, Victor M. Corman, Dieter Beule, Emanuel Wyler, Markus Landthaler, Benedikt Obermayer, Saskia von Stillfried, Peter Boor, Munevver Demir, Hans Wesselmann, Norbert Suttorp, Alexander Uhrig, Holger Mueller-Redetzky, Jacob Nattermann, Wolfgang M. Kuebler, Christian Meisel, Markus Ralser, Joachim L. Schultze, Anna C. Aschenbrenner, Charlotte Thibeault, Florian Kurth, Leif E. Sander, Nils Bluethgen, Birgit Sawitzki
Summary: Severe COVID-19 is associated with highly activated CD16(+) T cells that exhibit cytotoxic functions and contribute to endothelial injury. These CD16(+) T cells can degranulate and induce cytotoxicity through immune-complex-mediated mechanisms independent of the T cell receptor, which is not observed in other diseases. The presence of activated CD16(+) T cells and elevated levels of complement proteins upstream of C3a are associated with a fatal outcome of COVID-19, indicating the pathological role of enhanced cytotoxicity and complement activation in the disease.
Article
Medical Informatics
Jakob Steinfeldt, Thore Buergel, Lukas Loock, Paul Kittner, Greg Ruyoga, Julius Upmeier zu Belzen, Simon Sasse, Henrik Strangalies, Lara Christmann, Noah Hollmann, Benedict Wolf, Brian Ference, John Deanfield, Ulf Landmesser, Roland Eils
Summary: In this study, a neural network-based risk model (NeuralCVD) was developed and validated to estimate cardiovascular risk for primary prevention. The model integrates polygenic and clinical predictors and improves risk discrimination compared to established clinical scores and a Cox model. The findings highlight the importance of genetic information in identifying individuals with a high genetic predisposition for preventive interventions.
LANCET DIGITAL HEALTH
(2022)