Article
Biochemistry & Molecular Biology
Maximilien Franck, Juan de Toro-Martin, Thibault V. Varin, Veronique Garneau, Genevieve Pilon, Denis Roy, Patrick Couture, Charles Couillard, Andre Marette, Marie-Claude Vohl
Summary: Numerous studies have found that diets rich in phenolic compounds are beneficial for immune-metabolic health, but the effects vary among individuals and the mechanisms are not well understood. This study used transcriptomic analysis to identify two subgroups of responders and non-responders to raspberry consumption based on whole-blood RNAseq data. Responders showed a significant decrease in triglycerides, cholesterol, and C-reactive protein levels, and had distinct gene expression and microbiota profiles compared to non-responders. The transcriptomic approach used in this study provides a promising framework for understanding the inter-individual variability in the impact of foods on immune-metabolic health.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Stephanie M. Zimmerman, Robin Fropf, Bridget R. Kulasekara, Maddy Griswold, Oliver Appelbe, Arya Bahrami, Rich Boykin, Derek L. Buhr, Kit Fuhrman, Margaret L. Hoang, Quoc Huynh, Lesley Isgur, Andrew Klock, Alecksandr Kutchma, Alexa E. Lasley, Yan Liang, Jill McKay-Fleisch, Jeffrey S. Nelson, Karen Nguyen, Erin Piazza, Aric Rininger, Daniel R. Zollinger, Michael Rhodes, Joseph M. Beechem
Summary: Emerging spatial profiling technology allows high-plex molecular profiling in biological tissues while preserving the spatial and morphological context of gene expression. By expanding the chemistry for the Digital Spatial Profiling platform, researchers have successfully quantified whole transcriptomes in human and mouse tissues, enabling applications in cancer research, molecular pathology, and developmental biology.
Article
Chemistry, Analytical
Kerwin Kwek Zeming, Ri Lu, Kai Lee Woo, Guoyun Sun, Kai Yun Quek, Lih Feng Cheow, Chia-Hung Chen, Jongyoon Han, Shir Lynn Lim
Summary: This study successfully achieved multiplexed analysis of single-cell enzyme secretion from leukocytes through a fully integrated system, analyzing from undiluted blood samples without preprocessing steps, potentially elucidating immune response states.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Wenjuan Ding, Jiajia Tu, Huaran Zhang, Xiaoyi Wei, Jianhua Ju, Qinglian Li
Summary: The study presents the complete genome sequence of Streptomyces koyangensis SCSIO 5802, revealing its potential to produce a variety of natural products. By inactivating biosynthetic machineries, researchers were able to stimulate the production of two polycyclic tetramate macrolactams and discover a novel compound. This approach demonstrates an effective method to activate cryptic biosynthetic gene clusters and uncover new bioactive metabolites through genome mining and metabolic profiling methods.
Article
Biochemical Research Methods
Tobias Tekath, Martin Dugas
Summary: DTUrtle is a software package for analyzing bulk and single-cell RNA-seq datasets, allowing for transcript-level differential analysis with various result aggregation, visualization options, and a novel detection probability score. Successfully applied to human and mouse data, potential applications include identifying cell-type specific transcript isoforms.
Article
Biochemistry & Molecular Biology
Simone Altmann, Eva Rico, Sandra Carvalho, Melanie Ridgway, Anna Trenaman, Hannah Donnelly, Michele Tinti, Susan Wyllie, David Horn
Summary: This study reports a simple method for rapid and precise editing of priority drug targets in trypanosomatids. By targeting and editing drug targets, combined with sequencing technology, potential impacts on drug efficacy can be assessed quickly.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Medicine, Research & Experimental
Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta, Fatemeh Vahidnezhad, Zahra Saffarian, Kambiz Kamyab-Hesari, Mohammad Tolouei, Niloofar Faraji, Seyyede Zeinab Azimi, Ghazal Namdari, Parvin Mansouri, Jean-Laurent Casanova, Vivien Beziat, Emmanuelle Jouanguy, Jouni Uitto, Hassan Vahidnezhad
Summary: HPVs are DNA viruses classified into 5 genera, including approximately 450 types. In patients with an inborn error of immunity, some species of beta-HPVs can cause epidermodysplasia verruciformis (EV), characterized by stubborn cutaneous warts and skin cancer. This study identified new genetic mutations in TMC6, TMC8, and CIB1 genes and implicated new HPV subtypes in the development of typical EV.
Article
Biotechnology & Applied Microbiology
Nir Ben-Chetrit, Xiang Niu, Ariel D. D. Swett, Jesus Sotelo, Maria S. S. Jiao, Caitlin M. M. Stewart, Catherine Potenski, Paulius Mielinis, Patrick Roelli, Marlon Stoeckius, Dan A. A. Landau
Summary: Spatial transcriptomics and proteomics have independently revolutionized our understanding of complex biological processes by providing complementary information. However, integrating these modalities in experiments has been limited. To address this, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for simultaneous high-throughput spatial transcriptomics and protein profiling. SPOTS significantly improves signal resolution, cell clustering, and enhances the discovery power for differential gene expression analysis across tissue regions compared to unimodal measurements.
NATURE BIOTECHNOLOGY
(2023)
Article
Agricultural Engineering
Aatif Rashid, Manu Khajuria, Villayat Ali, Sheenam Faiz, Sumit Jamwal, Dhiraj Vyas
Summary: This study identified 48 WRKY transcription factors in Cannabis sativa through genome research, and classified them into different groups based on physiochemical and phylogeny analysis. The findings showed that CsWRKY genes remained conserved during evolution, and their upstream sequences contained stress-related elements. Functional analysis and protein-protein interaction revealed the regulatory network of CsWRKY. Additionally, several CsWRKY genes were found to play a potential role in inflorescence development and cannabinoid regulation.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Simona Nemska, Simone Serio, Veronica Larcher, Giulia Beltrame, Nicola Marcello Portinaro, Marie-Louise Bang
Summary: Cerebral palsy is the most common movement disorder in children, caused by non-progressive brain lesions. RNA-sequencing analysis showed different gene expression patterns in CP patients undergoing tendon lengthening surgery, especially in tetraplegic patients. Overall, tetraplegic CP patients displayed increased collagen synthesis and ECM turnover, without activation of inflammatory and apoptotic pathways.
Article
Multidisciplinary Sciences
Lyrialle W. Han, Yuanyuan Shi, Alison Paquette, Lu Wang, Theo K. Bammler, Qingcheng Mao
Summary: Pregnancy and the microbiome have complex interactions that affect host metabolism, particularly in hepatic metabolic processes. Research has shown that the presence or absence of the microbiome can impact specific metabolic pathways in pregnant mice, providing new insights into the role of the microbiome in modulating metabolic processes during pregnancy.
Article
Biochemical Research Methods
Niels M. Leijten, Petra Bakker, Herman P. Spaink, Jeroen den Hertog, Simone Lemeer
Summary: Thermal proteome profiling (TPP) enables unbiased detection of drug-target protein engagements in vivo. By using whole zebrafish embryo lysate, this study identified potential protein targets of napabucasin, including oxidoreductase PORA, which may affect Stat3 signaling.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Oncology
Cheonghwa Lee, Ha Nui Kim, Jung Ah Kwon, Jinha Hwang, Ji-Ye Park, Ok Sarah Shin, Soo-Young Yoon, Jung Yoon
Summary: Complex karyotype (CK) is associated with poor prognosis in AML and MDS-EB, and dysregulated gene expression may be involved. We identified a 10-gene signature (CKS) that accurately predicts CK and is associated with shorter overall survival.
Article
Oncology
Francois Bertucci, Vincent Niziers, Alexandre de Nonneville, Pascal Finetti, Lena Mescam, Olivier Mir, Antoine Italiano, Axel Le Cesne, Jean-Yves Blay, Michele Ceccarelli, Davide Bedognetti, Daniel Birnbaum, Emilie Mamessier
Summary: This study investigated the impact of immunologic constant of rejection (ICR) on the prognostic assessment of early-stage soft-tissue sarcomas (STS). The results showed that ICR signature was associated with patient age, pathological type, and tumor depth, and remained independently associated with metastasis-free survival (MFS) in multivariate analysis. A prognostic clinicogenomic model was also built, integrating ICR, Complexity Index in Sarcomas (CINSARC), and pathological type, and different systemic therapies were suggested for each prognostic group.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Physiology
Kasja Malkoc, Stefania Casagrande, Michaela Hau
Summary: Metabolic rate is a key ecological variable quantifying energy expenditure in organisms. Blood-based cMR measurement offers advantages in estimating metabolism with minimal disturbance, but the correlation with woMR needs further investigation. Individual stress responses should be considered when measuring metabolic rate.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Immunology
Aline H. de Nooijer, Inge Grondman, Nico A. F. Janssen, Mihai G. Netea, Loek Willems, Frank L. van de Veerdonk, Evangelos J. Giamarellos-Bourboulis, Erik J. M. Toonen, Leo A. B. Joosten
Summary: In COVID-19 patients, activation of the complement system is associated with disease severity, mortality rate, and thromboembolic events. This suggests components of the complement system could serve as potential prognostic markers and therapeutic targets in COVID-19.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Matthew S. Buckland, James B. Galloway, Caoimhe Nic Fhogartaigh, Luke Meredith, Nicholas M. Provine, Stuart Bloor, Ane Ogbe, Wioleta M. Zelek, Anna Smielewska, Anna Yakovleva, Tiffeney Mann, Laura Bergamaschi, Lorinda Turner, Frederica Mescia, Erik J. M. Toonen, Carl-Philipp Hackstein, Hossain Delowar Akther, Vinicius Adriano Vieira, Lourdes Ceron-Gutierrez, Jimstan Periselneris, Sorena Kiani-Alikhan, Sofia Grigoriadou, Devan Vaghela, Sara E. Lear, M. Estee Torok, William L. Hamilton, Joanne Stockton, Josh Quick, Peter Nelson, Michael Hunter, Tanya I. Coulter, Lisa Devlin, John R. Bradley, Kenneth G. C. Smith, Willem H. Ouwehand, Lise Estcourt, Heli Harvala, David J. Roberts, Ian B. Wilkinson, Nick Screaton, Nicholas Loman, Rainer Doffinger, Paul A. Lyons, B. Paul Morgan, Ian G. Goodfellow, Paul Klenerman, Paul J. Lehner, Nicholas J. Matheson, James E. D. Thaventhiran
NATURE COMMUNICATIONS
(2020)
Review
Immunology
Felix Poppelaars, Elena Goicoechea de Jorge, Ilse Jongerius, Antje J. Baeumner, Mark-Steven Steiner, Mihaly Jozsi, Erik J. M. Toonen, Diana Pauly
Summary: The human Factor H (FH) family is linked to various diseases, with controversies and discrepancies in its functional roles and quantification, requiring interdisciplinary collaboration to address these challenges.
FRONTIERS IN IMMUNOLOGY
(2021)
Correction
Immunology
Felix Poppelaars, Elena Goicoechea de Jorge, Ilse Jongerius, Antje J. Baeumner, Mark-Steven Steiner, Mihaly Jozsi, Erik J. M. Toonen, Diana Pauly
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pratiti Banerjee, Bert Veuskens, Elena Goicoechea de Jorge, Mihaly Jozsi, Antje J. Baeumner, Mark-Steven Steiner, Richard B. Pouw, Erik J. M. Toonen, Diana Pauly, Felix Poppelaars
Summary: Complement targeted-therapies have become a validated and accepted treatment option, revitalizing the field and bringing attention to complement therapeutics. However, there is a lack of standardized tools for complement testing. Measurement of complement protein levels can assist in assessing disease risk and predicting disease progression and treatment response.
MOLECULAR IMMUNOLOGY
(2022)
Article
Immunology
Ricardo J. M. G. E. Brandwijk, Marloes A. H. M. Michels, Mara van Rossum, Aline H. de Nooijer, Per H. Nilsson, Wieke C. C. de Bruin, Erik J. M. Toonen
Summary: The complement system is crucial in disease pathogenesis and its assessment is essential for monitoring disease progression and therapy response. However, standardized sampling and assay procedures for complement analysis remain challenging. This study highlights the importance of using appropriate sample types and techniques to avoid misinterpretation of complement biomarkers and to enable accurate comparison between studies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Gyorgy Sinkovits, Janos Schnur, Lisa Hurler, Petra Kiszel, Zita Z. Prohaszka, Pal Sik, Erika Kajdacsi, Laszlo Cervenak, Veronika Maraczi, Mate David, Borbala Zsigmond, Eva Rimanoczy, Csaba Bereczki, Loek Willems, Erik J. M. Toonen, Zoltan Prohaszka
Summary: Multisystem inflammatory syndrome in children (MIS-C) is a rare and life-threatening complication of SARS-CoV-2 infection. This syndrome is characterized by high fever, inflammation, and shock-like symptoms. Activation of immune cells and inflammation markers play a crucial role in the pathogenesis, and treatment with intravenous immunoglobulin leads to improvement of the disease. Complement system activation is closely related to the disease activity and its reduction is associated with rapid improvement after treatment.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Lisa Hurler, Erik J. M. Toonen, Erika Kajdacsi, Bregje van Bree, Ricardo J. M. G. E. Brandwijk, Wieke de Bruin, Paul A. Lyons, Laura Bergamaschi, Gyorgy Sinkovits, Laszlo Cervenak, Reinhard Wuerzner, Zoltan Prohaszka
Summary: This study aimed to develop validated immunoassays for detecting C1s/C1-INH and MASP-1/C1-INH complex levels and investigate their potential as markers for early classical and lectin pathway activation. The results showed that these complexes can reliably measure concentrations in healthy and diseased individuals and are increased in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Lisa Hurler, Agnes Szilagyi, Federica Mescia, Laura Bergamaschi, Blanka Mezo, Gyorgy Sinkovits, Marienn Reti, Veronika Mueller, Zsolt Ivanyi, Janos Gal, Laszlo Gopcsa, Peter Remenyi, Beata Szathmary, Botond Lakatos, Janos Szlavik, Ilona Z. Bobek, Zita Prohaszka, Zsolt Forhecz, Dorottya Csuka, Erika Kajdacsi, Laszlo Cervenak, Petra Kiszel, Tamas Masszi, Istvan Valyi-Nagy, Reinhard A. Wuerzner, Paul Lyons, Erik J. M. Toonen, Zoltan Prohaszka
Summary: The lectin pathway is activated in acute COVID-19, but the role of MBL in COVID-19 is still not fully understood.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Mads Lamm Larsen, Anne Troldborg, Erik J. M. Toonen, Lisa Hurler, Zoltan Prohaszka, Laszlo Cervenak, Annette Gudmann Hansen, Steffen Thiel
Summary: This study aims to differentiate between classical or lectin pathway-mediated complement activation in SLE patients by quantifying pathway-specific protein complexes. The classical pathway is activated in active SLE disease, whereas activation of the lectin pathway might be more specific to disease manifestations like lupus nephritis.
CLINICAL AND EXPERIMENTAL IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Federica Mescia, Shaghayegh Bayati, Elisabeth Brouwer, Peter Heeringa, Erik J. M. Toonen, Marijke Beenes, Miriam J. Ball, Andrew J. Rees, Renate Kain, Paul A. Lyons, Peter Nilsson, Elisa Pin
Summary: This study aimed to analyze the autoantibody repertoire of AAV patients using antigen arrays and identified previously unreported antibodies linked to the disease and observed possible associations between anti-kinesin antibodies and clinically relevant features within AAV patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Stejara A. Netea, Giske Biesbroek, Diana van Stijn, Hanna Ijspeert, Caspar I. van der Made, Machiel H. Jansen, Judy Geissler, J. M. (Merlijn) van den Berg, Martijn van der Kuip, Mariken P. Gruppen, Dieneke Schonenberg-Meinema, Berber Kapitein, A. M. (Marceline) Tutu van Furth, Sietse Q. Nagelkerke, Dasja Pajkrt, Frans B. Plotz, M. E. J. (Lisette) den Boer, Gijs W. Landman, Marlies A. van Houten, Ines Goetschalckx, Erik J. M. Kawasaki Study Grp, Erik J. M. Toonen, Frank L. van de Veerdonk, Irene M. Kuipers, Willem A. Dik, Taco W. Kuijpers
Summary: Compared with KD, MIS-C in children with SARS-CoV-2 has similar clinical features, and both diseases have been found to have anti-cytokine autoantibodies (ACAAs), especially antibodies against IFN-γ. In addition, in MIS-C, levels of anti-IL-17A and anti-IL-22 are negatively correlated with ICU admission. The study results indicate that markers of endothelial activation (E-selectin, angiopoietin-2), as well as innate and adaptive immune responses, are upregulated in both KD and MIS-C. ACAAs are present in both diseases and, although only partially neutralizing, their transient presence and increased levels in non-ICU patients may suggest a dampening role on inflammation.
Article
Critical Care Medicine
Aline H. de Nooijer, Antigone Kotsaki, Eleftheria Kranidioti, Matthijs Kox, Peter Pickkers, Erik J. M. Toonen, Evangelos J. Giamarellos-Bourboulis, Mihai G. Netea
Summary: This study investigated complement factors in 209 hospitalized sepsis patients and found that the concentration of complement factors was significantly increased in severely ill sepsis patients. However, there was no significant correlation between complement factors and other inflammatory biomarkers.
Article
Geriatrics & Gerontology
Yannick van Sleen, Sudarshan A. Shetty, Marieke van der Heiden, Milou C. A. Venema, Nicolas Gutierrez-Melo, Erik J. M. Toonen, Josine van Beek, Anne-Marie Buisman, Debbie van Baarle, Delphine Sauce
Summary: Frailty is an age-associated state characterized by increased vulnerability and decreased resilience. Inflammageing markers, particularly those reflecting innate immune activation, are related to frailty, indicating a link between health decline and low-grade inflammation.
Article
Rheumatology
Yannick van Sleen, Philip Therkildsen, Berit Dalsgaard Nielsen, Kornelis S. M. van der Geest, Ib Hansen, Peter Heeringa, Marcel D. Posthumus, Maria Sandovici, Erik J. M. Toonen, Jannik Zijlstra, Annemieke M. H. Boots, Ellen-Margrethe Hauge, Elisabeth Brouwer
Summary: This study conducted in two independent international cohorts shows that the angiopoietin-2/-1 ratios and MMP-3 levels can potentially identify GCA in patients presenting with PMR. Furthermore, platelet counts may be used to distinguish GCA from GCA mimicry patients.
ARTHRITIS RESEARCH & THERAPY
(2022)