Article
Multidisciplinary Sciences
Fabian Stahl, Ina Schmitt, Philip Denner, Laura de Boni, Ullrich Wuellner, Peter Breuer
Summary: The study suggests that simvastatin may be a potential treatment for SCA3 and increases ATXN3 protein levels by directly binding to the ATXN3 promoter.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Xi He, Shuo Quan, Min Xu, Silveria Rodriguez, Shih Lin Goh, Jiajie Wei, Arthur Fridman, Kenneth A. Koeplinger, Steve S. Carroll, Jay A. Grobler, Amy S. Espeseth, David B. Olsen, Daria J. Hazuda, Dai Wang
Summary: This study successfully constructed a noninfectious SARS-CoV-2 reporter replicon for deciphering viral replication mechanisms and evaluating antiviral drugs, and developed a high-throughput antiviral assay. Significant differences in the potencies of several SARS-CoV-2 inhibitors in different cell lines were observed, highlighting the importance of testing compounds in multiple cell culture models for discovering antivirals capable of inhibiting viral replication in vivo.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Pharmacology & Pharmacy
Nikunj M. Shukla, Fumi Sato-Kaneko, Shiyin Yao, Minya Pu, Michael Chan, Fitzgerald S. Lao, Yukiya Sako, Tetsuya Saito, Karen Messer, Tomoko Hayashi, Howard B. Cottam, Maripat Corr, Dennis A. Carson
Summary: Extracellular vesicles play a crucial role in intercellular communication and immune regulation. Researchers have identified small molecule compounds that can enhance the immunogenicity of vaccines by increasing the release of extracellular vesicles. The compounds were screened and validated through multiple assays, leading to the discovery of potential vaccine adjuvants.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Julian Hackler, Kamil Demircan, Thilo Samson Chillon, Qian Sun, Nino Geisler, Michael Schupp, Kostja Renko, Lutz Schomburg
Summary: Selenium is an essential trace element that affects the expression of SELENOP. A drug screening was performed to identify inhibitors of SELENOP expression, and resveratrol was found to be the most potent inhibitor. The results suggest that resveratrol may increase liver Se levels and selenoprotein expression.
Article
Pharmacology & Pharmacy
Ningning Tang, Ling Li, Fei Xie, Ying Lu, Zifan Zuo, Hao Shan, Quan Zhang, Lianwen Zhang
Summary: Inhibition of cellular O-GlcNAcylation can suppress proliferation and migration of cancer cells, leading to a new avenue for cancer therapy. A cell-based fluorescent reporter was developed to sense changes in cellular O-GlcNAcylation, allowing for identification of natural compounds such as sesamin that inhibit O-GlcNAcylation and migration of cancer cells.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2021)
Article
Medicine, Research & Experimental
Emma Cretin, Priscilla Lopes, Elodie Vimont, Takashi Tatsuta, Thomas Langer, Anastasia Gazi, Martin Sachse, Patrick Yu-Wai-Man, Pascal Reynier, Timothy Wai
Summary: Mutations in OPA1 can cause DOA or DOA+ with severe neurological deficits, while depletion of PGS1 may help restore mitochondrial morphology and improve defects.
EMBO MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Ziva Svab, Luca Braga, Corrado Guarnaccia, Ivan Labik, Jeremias Herzog, Marco Baralle, Mauro Giacca, Natasa Skoko
Summary: In this study, several human miRNAs were identified to increase specific and overall production of Erythropoietin and Etanercept in CHO cells. Overexpression of miR-574-3p was found to improve productivity by up to 2-fold, with p300 identified as a main target. The findings highlight the importance of genomic sequences in pri-miRNA processing, offering a cost-effective strategy for efficient miRNA engineering in CHO cells.
Article
Engineering, Chemical
Andreas Mollebjerg, Agata Zarebska, Henrik Bangso Nielsen, Lea Benedicte Skov Hansen, Sebastian R. Sorensen, Bozena Seredynska-Sobecka, Loreen O. Villacorte, Klaus Gori, Lorena Gonzalez Palmen, Rikke Louise Meyer
Summary: Biofouling is a widespread problem in industrial systems, such as reverse osmosis (RO) desalination units, where biofilms impede water flow. Enzymes have shown promise as non-damaging and environmentally friendly cleaning agents for biofilms, but identifying effective enzymes is challenging. To overcome this, a flexible screening platform was developed to directly evaluate enzyme treatment on fouled RO membranes. This platform identified enzymes, including proteases, lipases, DNase, cellulolytic enzymes, and pectin-degrading enzymes, that effectively degraded biofilms on RO membranes. The most effective enzyme formulations outperformed chemical cleaning agents, removing 45% of the biofilm compared to 0%-19% for chemicals (p <= 0.001), highlighting the potential of enzymes as replacements or complements to chemical cleaning. The screening platform proved to be a powerful tool for studying and combating biofilms in various applications.
Article
Oncology
Chelsea Mayoh, Jie Mao, Jinhan Xie, Gabor Tax, Shu-Oi Chow, Roxanne Cadiz, Karina Pazaky, Paulette Barahona, Pamela Ajuyah, Peter Trebilcock, Angela Malquori, Kate Gunther, Anica Avila, Doo Young Yun, Stephanie Alfred, Anjana Gopalakrishnan, Alvin Kamili, Marie Wong, Mark J. Cowley, Sophie Jessop, Loretta M. S. Lau, Toby N. Trahair, David S. Ziegler, Jamie I. Fletcher, Andrew J. Gifford, Maria Tsoli, Glenn M. Marshall, Michelle Haber, Vanessa Tyrrell, Timothy W. Failes, Greg M. Arndt, Richard B. Lock, Paul G. Ekert, M. Emmy M. Dolman
Summary: One-third of pediatric cancer patients enrolled in precision medicine programs do not receive therapeutic recommendations from molecular profiling. In order to find potential strategies for treating high-risk pediatric patients, a study conducted in vitro screening of 125 patient-derived samples against a library of 126 anticancer drugs. The results showed that high-throughput drug screening (HTS) can identify effective biomarker-driven therapeutic strategies for high-risk pediatric cancers.
Article
Virology
Kang Ning, Anuradha Roy, Fang Cheng, Peng Xu, Steve Kleiboeker, Carlos R. Escalante, Jingxin Wang, Jianming Qiu
Summary: This study developed a high-throughput screening assay for identifying antivirals against B19V replication and discovered a purine derivative that exhibited significant antiviral activity against B19V infection.
JOURNAL OF VIROLOGY
(2022)
Article
Immunology
Rodrigo Vazquez-Lombardi, Johanna S. Jung, Fabrice S. Schlatter, Anna Mei, Natalia Rodrigues Mantuano, Florian Bieberich, Kai-Lin Hong, Jakub Kucharczyk, Edo Kapetanovic, Erik Aznauryan, Cedric R. Weber, Alfred Zippelius, Heinz Laubli, Sai T. Reddy
Summary: A major challenge in TCR immunotherapy is finding natural TCRs with high activity and specificity to tumor antigens. In this study, we developed a method called TCR-Engine to successfully engineer synthetic TCRs with increased potency and specificity to a clinically relevant tumor antigen. We validated their potential for translation through in vitro and in vivo assessments of safety and efficacy.
Article
Oncology
Sigve Nakken, Vladislav Saveliev, Oliver Hofmann, Pal Moller, Ola Myklebost, Eivind Hovig
Summary: High-throughput germline genetic testing is increasingly valuable in cancer care, and the open-source CPSR computational workflow can generate structured reports highlighting the therapeutic, prognostic, and diagnostic relevance of germline variants in cancer predisposition genes. The tool provides flexibility in selecting genes to include in the report, while maintaining consistency with ACMG standards.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Biology
Robert Coukos, David Yao, Mateo Sanchez, Eric T. Strand, Meagan E. Olive, Namrata D. Udeshi, Jonathan S. Weissman, Steven A. Carr, Michael C. Bassik, Alice Y. Ting
Summary: The study demonstrates that gene perturbation technology combined with HiLITR tool can be used to explore protein trafficking processes by converting protein colocalization into a transcription factor driving expression of selected genes. By using HiLITR with FACS screening, genes that influence the trafficking of mitochondrial and ER tail-anchored proteins were identified, revealing the roles of SUMO E1 component SAE1 and EMC10 in mitochondrial and ER systems.
Article
Cell Biology
Hellen Weinschutz Mendes, Uma Neelakantan, Yunqing Liu, Sarah E. Fitzpatrick, Tianying Chen, Weimiao Wu, April Pruitt, David S. Jin, Priyanka Jamadagni, Marina Carlson, Cheryl M. Lacadie, Kristen D. Enriquez, Ningshan Li, Dejian Zhao, Sundas Ijaz, Catalina Sakai, Christina Szi, Brendan Rooney, Marcus Ghosh, Ijeoma Nwabudike, Andrea Gorodezky, Sumedha Chowdhury, Meeraal Zaheer, Sarah McLaughlin, Joseph M. Fernandez, Jia Wu, Jeffrey A. Eilbott, Brent Vander Wyk, Jason Rihel, Xenophon Papademetris, Zuoheng Wang, Ellen J. Hoffman
Summary: This study performs parallel in vivo functional analysis of 10 ASD genes at the behavioral, structural, and circuit levels in zebrafish mutants, revealing both unique and overlapping effects of gene loss of function. Whole-brain mapping identifies the forebrain and cerebellum as the most significant contributors to brain size differences, while regions involved in sensory-motor control, particularly dopaminergic regions, are associated with altered baseline brain activity. Finally, a global increase in microglia resulting from ASD gene loss of function in select mutants implicates neuroimmune dysfunction as a key pathway relevant to ASD biology.
Article
Neurosciences
Areej Mesleh, Hanan Ehtewish, Katie Lennard, Houari B. Abdesselem, Fouad Al-Shaban, Julie Decock, Nehad M. Alajez, Abdelilah Arredouani, Mohamed M. Emara, Omar Albagha, Lawrence W. Stanton, Sara A. Abdulla, Jonathan M. Blackburnand, Omar M. A. El-Agnaf
Summary: This study used high-throughput KoRectly Expressed (KREX) i-Ome protein-array technology to screen serum samples from 93 cases with ASD and 28 healthy controls. The aim was to identify autoantibodies with differential expressions in ASD and gain insights into their biological significance in the context of ASD pathogenesis.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Shanna Dewaele, Louis Delhaye, Boel De Paepe, Eric James de Bony, Jilke De Wilde, Katrien Vanderheyden, Jasper Anckaert, Nurten Yigit, Justine Nuytens, Eveline Vanden Eynde, Joel Smet, Maxime Verschoore, Fariba Nemati, Didier Decaudin, Manuel Rodrigues, Peihua Zhao, Aart Jochemsen, Eleonora Leucci, Jo Vandesompele, Jo Van Dorpe, Jean-Christophe Marine, Rudy Van Coster, Sven Eyckerman, Pieter Mestdagh
Summary: The inhibition of SAMMSON in uveal melanoma cells has shown to impair cell growth and viability, induce apoptosis, and affect protein translation levels, highlighting its potential as a therapeutic target. This study demonstrates the essential role of SAMMSON expression in uveal melanoma cell survival, suggesting ASO-mediated silencing of SAMMSON as a promising treatment strategy for both primary and metastatic uveal melanoma patients.
Article
Biochemistry & Molecular Biology
Gaelle Houthaeve, Gerardo Garcia-Diaz Barriga, Stephan Stremersch, Herlinde De Keersmaecker, Juan Fraire, Jo Vandesompele, Pieter Mestdagh, Stefaan De Smedt, Kevin Braeckmans, Winnok H. De Vos
Summary: The study investigates the effects of VNB photoporation on cell homeostasis, finding that A-type lamins are upregulated after photoporation and contribute to the recovery of the nucleus. Selective depletion of A-type lamins reduces cell viability, while stimulation of LMNA transcription increases the survival rate of successfully transfected cells.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Medical Laboratory Technology
Daniel Evans, Simon Cowen, Martin Kammel, Denise M. O'Sullivan, Graham Stewart, Hans-Peter Grunert, Jacob Moran-Gilad, Jasper Verwilt, Jiwon In, Jo Vandesompele, Kathryn Harris, Ki Ho Hong, Nathaniel Storey, Suzie Hingley-Wilson, Ulf Duhring, Young-Kyung Bae, Carole A. Foy, Julian Braybrook, Heinz Zeichhardt, Jim F. Huggett
Summary: The study found poor interlaboratory reproducibility when using Cq values as clinical cutoffs or diagnostic performance targets, recommending calibrated copy-based units as more reproducible alternatives. Additionally, discrepancies in diagnostic performance may change relative to the effective reproduction number, emphasizing the importance of considering patient population disparities over time when evaluating or deploying diagnostic tests, particularly in emergency situations such as a evolving pandemic.
CLINICAL CHEMISTRY
(2022)
Review
Medicine, General & Internal
Daniela Drandi, Philippe Decruyenaere, Martina Ferrante, Fritz Offner, Jo Vandesompele, Simone Ferrero
Summary: This review aims to provide a comprehensive overview of molecular biomarkers in Waldenstrom Macroglobulinemia (WM) and IgM gammopathies, and explore their potential applications in precision medicine.
Meeting Abstract
Oncology
K. Schoofs, F. Avila Cobos, A. Philippron, J. Anckaert, P. Pattyn, J. Vandesompele, K. De Preter
ANNALS OF ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anneleen Decock, David Creytens, Steve Lefever, Joni Van der Meulen, Jasper Anckaert, Ariane De Ganck, Jill Deleu, Bram De Wilde, Carolina Fierro, Scott Kuersten, Manuel Luypaert, Isabelle Rottiers, Gary P. Schroth, Sandra Steyaert, Katrien Vanderheyden, Eveline Vanden Eynde, Kimberly Verniers, Joke Verreth, Jo Van Dorpe, Jo Vandesompele
Summary: This study demonstrates that mRNA capture sequencing improves the detection rate of pathognomonic fusions in sarcomas and enables the identification of novel and secondary fusion transcripts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
Philippe Decruyenaere, Kimberly Verniers, Franco Poma-Soto, Jo Van Dorpe, Fritz Offner, Jo Vandesompele
Summary: This study compared the impact of three RNA extraction methods on yield, quality, and sequencing-based gene expression results in FFPE samples. The results showed that methods B and C outperformed method A, resulting in higher fractions of uniquely mapped reads, an increased number of detectable genes, a lower fraction of duplicated reads, and better representation of the B-cell receptor repertoire. Caution should be applied when comparing and interpreting results obtained using different methods.
LABORATORY INVESTIGATION
(2023)
Article
Biochemical Research Methods
Celine Everaert, Jasper Verwilt, Kimberly Verniers, Niels Vandamme, Alvaro Marcos Rubio, Jo Vandesompele, Pieter Mestdagh
Summary: RNA sequencing is widely used for transcriptome analysis, but quantification of low-abundant transcripts remains challenging. Researchers have developed a strategy using high-affinity RNA-binding oligonucleotides to reduce the abundance of specific RNA transcripts in sequencing libraries. This method is efficient, reproducible, and can be easily integrated into existing RNA sequencing protocols, improving transcriptome coverage and complexity.
BIOLOGICAL PROCEDURES ONLINE
(2023)
Review
Biochemistry & Molecular Biology
Jasper Verwilt, Pieter Mestdagh, Jo Vandesompele
Summary: RNA sequencing has become influential in various research fields. However, the reverse transcription reaction in most protocols often leads to biases and artifacts in the resulting cDNA pool, which are overlooked in the literature. This review discusses these issues and provides solutions and good practices for RNA sequencing experiments, aiming to contribute to scientifically sound RNA studies.
Review
Medical Laboratory Technology
Matthijs Vynck, Yao Chen, David Gleerup, Jo Vandesompele, Wim Trypsteen, Antoon Lievens, Olivier Thas, Ward De Spiegelaere
Summary: Background partition classification is essential in digital PCR data analysis. This review provides an overview of available methods and their challenges, serving as a guide for practitioners. Strengths, weaknesses, and application gaps are discussed, stimulating method development.
CLINICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Lei Zhai, Anushree Balachandran, Rebecca Larkin, Janith A. Seneviratne, Sylvia A. Chung, Amit Lalwani, Shoma Tsubota, Dominik Beck, Kenji Kadomatsu, Anneleen Beckers, Kaat Durink, Katleen De Preter, Frank Speleman, Michelle Haber, Murray D. Norris, Alexander Swarbrick, Belamy B. Cheung, Glenn M. Marshall, Daniel R. Carter
Summary: Mitotic dysregulation is identified as a hallmark of tumor initiation in neuroblastoma and can be targeted by a combination therapy of antimitotic and pro-apoptotic compounds, leading to selective cell death in MYCN-driven neuroblastoma cell lines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alan Van Goethem, Jill Deleu, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Sanjeev A. Vasudevan, Fjoralba Zeka, Fleur Demuynck, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Jo Vandesompele, Tom Van Maerken
Summary: In this study, we evaluated whether circulating miRNAs can be used to monitor neuroblastoma tumor burden and treatment-induced changes in the tumor. We performed small RNA sequencing on serum samples from mice with neuroblastoma xenografts treated with idasanutlin or temsirolimus. We identified serum miRNAs that correlated with tumor tissue expression and tumor volume, as well as miRNAs that responded to p53 activation following idasanutlin treatment.
Article
Biochemistry & Molecular Biology
Vanessa Vermeirssen, Jill Deleu, Annelien Morlion, Celine Everaert, Jilke De Wilde, Jasper Anckaert, Kaat Durinck, Justine Nuytens, Muhammad Rishfi, Frank Speleman, Hanne Van Droogenbroeck, Kimberly Verniers, Maria Francesca Baietti, Maarten Albersen, Eleonora Leucci, Edward Post, Myron G. Best, Tom Van Maerken, Bram De Wilde, Jo Vandesompele, Anneleen Decock
Summary: This study developed a deconvolution framework to distinguish tumor-derived extracellular RNA (exRNA) from host RNA. Analysis of liquid biopsy samples from mice revealed that tumor-derived exRNA concentrations were not determined by plasma platelet levels, while host exRNA concentrations increased with platelet content. Additionally, there was a large variability in exRNA abundance and transcript content across individual mice. The detectability of tumor genes in plasma was largely correlated with RNA expression levels in the tumor tissue or cell line.
Article
Genetics & Heredity
Jill Deleu, Kathleen Schoofs, Anneleen Decock, Kimberly Verniers, Sofie Roelandt, Angie Denolf, Joke Verreth, Bram De Wilde, Tom Van Maerken, Katleen De Preter, Jo Vandesompele
Summary: This study establishes a framework to evaluate the performance of cfDNA/cfRNA co-purification kits and tests different kits under different plasma input volumes. The results demonstrate the advantage of combined quantification of cfDNA and cfRNA over separate quantification, which is crucial for increasing mutation detection sensitivity and improving disease detection and monitoring.