Review
Immunology
Sergi Torres-Puig, Vanesa Garcia, Kristian Staerk, Thomas E. Andersen, Jakob Moller-Jensen, John E. Olsen, Ana Herrero-Fresno
Summary: Uropathogenic Escherichia coli (UPEC) is the main cause of urinary tract infection (UTI), and the increase in antibiotic resistance poses challenges for UTI treatment. The use of 'omics' technologies in studying UPEC has revealed numerous factors that contribute to UPEC's ability to cause disease. This review summarizes the findings of 'omics' studies on UPEC pathogenesis and discusses current and future challenges.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Zhengdong Gao, Yaxiao Liu, Lekai Zhang, Zizhuo Yang, Linchen Lv, Shuai Wang, Lipeng Chen, Nan Zhou, Yaofeng Zhu, Xuewen Jiang, Benkang Shi, Yan Li
Summary: This study explores the interaction between nociceptor neurons and the bladder immune system during urinary tract infections (UTIs). The researchers found that uropathogenic Escherichia coli (UPEC) and its pathogenic factor directly stimulate nociceptor neurons, causing the neurons to release calcitonin gene-related peptide (CGRP) and suppress immune responses. By blocking neuronal inhibition, UTI can be prevented.
JOURNAL OF INFLAMMATION RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Georgia I. Nasi, Konstantina I. Georgakopoulou, Marilena K. Theodoropoulou, Nikos C. Papandreou, Evangelia D. Chrysina, Paraskevi L. Tsiolaki, Vassiliki A. Iconomidou
Summary: Type I fimbriae, composed of four subunits, play a critical role in uropathogenic Escherichia coli (UPEC) infections, with the FimH adhesin at the fimbrial tip as the key component. We propose that the amyloidogenic potential of FimH can be used for developing therapeutic agents against Urinary Tract Infections (UTIs). By identifying aggregation-prone regions (APRs) and synthesizing corresponding peptide-analogues, we demonstrate that these molecules can interfere with FimH folding or compete for the mannose-binding pocket, making them promising antimicrobial candidates.
Article
Microbiology
Manuel G. Ballesteros-Monrreal, Margarita M. P. Arenas-Hernandez, Edwin Barrios-Villa, Josue Juarez, Maritza Lizeth alvarez-Ainza, Pablo Taboada, Rafael de la Rosa-lopez, Enrique Bolado-Martinez, Dora Valencia
Summary: Urinary tract infections caused by Uropathogenic Escherichia coli in women in Sonora, Mexico show diverse bacterial morphotypes, virulence genes, and phenotypes, with high resistance to various antibiotics. The presence of morphotypes in urine sediment is crucial in urine analysis, and the clinical isolates of UPEC in this study have the potential to cause different types of UTIs.
Article
Immunology
Jennifer Jones, Craig P. Murphy, Roy D. Sleator, Eamonn P. Culligan
Summary: Advancements in bacterial culturing and DNA sequencing techniques have unveiled a previously unknown urinary tract microbiome (urobiome). The potential significance of this microbial community in health and disease, especially in the context of urinary tract infections (UTIs), is being increasingly recognized. Research shows that the urobiome plays a crucial role in the body's innate immune defenses and could be a valuable resource for developing alternative treatments and control strategies for UTIs.
MICROBIAL PATHOGENESIS
(2021)
Article
Medicine, Research & Experimental
Wenkun Fu, Wei Wang, Lunzhi Yuan, Yanzhen Lin, Xiumin Huang, Rirong Chen, Minping Cai, Che Liu, Liqiang Chen, Ming Zhou, Kun Wu, Huan Zhao, Dequan Pan, Jian Ma, Junping Hong, Bingke Zhai, Yali Zhang, Zhibo Kong, Yingbin Wang, Yixin Chen, Quan Yuan, Huachen Zhu, Tong Cheng, Yi Guan, Ningshao Xia
Summary: This study utilized a humanized mouse model with human lung xenografts to investigate SARS-CoV-2 infection. The results showed that the human lung xenografts closely resembled normal human lung structure, supported efficient replication and spread of SARS-CoV-2, caused severe lung damage, and induced a strong pro-inflammatory response. Treatment with IFN-alpha effectively inhibited viral replication in the lung xenografts. This model proves to be a valuable tool for studying SARS-CoV-2 lung infection pathogenesis and evaluating potential antiviral therapies.
Article
Public, Environmental & Occupational Health
Vanesa Garcia, Luz Leston, Ana Parga, Isidro Garcia-Menino, Javier Fernandez, Ana Otero, John E. Olsen, Ana Herrero-Fresno, Azucena Mora
Summary: This study investigated 31 strains of Escherichia coli from different sources using genomic comparison, bladder-cell, and biofilm formation assays. It found that animal-derived and human extraintestinal infection strains had high genomic similarity and exhibited similar pathogenic characteristics in cell and biofilm assays. These results highlight the potential role of food-producing animals as a source of urinary tract infections.
Article
Multidisciplinary Sciences
Jiehan Li, Christopher Jin, Stefan Gustafsson, Abhiram Rao, Martin Wabitsch, Chong Y. Park, Thomas Quertermous, Joshua W. Knowles, Ewa Bielczyk-Maczynska
Summary: Adipogenesis is the process of fat-specific progenitor cells differentiating into adipocytes that perform key metabolic functions of adipose tissue. This study provides a single-cell RNA-Sequencing dataset of adipogenic differentiation in 3T3-L1 and SGBS cells, allowing for comparative analysis and understanding of cell-to-cell variability in these widely used in vitro models.
Article
Microbiology
Laurens E. Zandbergen, Thomas Halverson, Jolanda K. Brons, Alan J. Wolfe, Marjon G. J. de Vos
Summary: The urinary tract is a poorly studied microbial niche where a microbiota exists, but the interactions between species and their impact on infections are still unclear. This study explores how uropathogens and resident bacteria in the urinary tract affect each other's growth, with potential implications for understanding urinary microbial ecosystems.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Wendiao Zhang, Ming Zhang, Zhenhong Xu, Hongye Yan, Huimin Wang, Jiamei Jiang, Juan Wan, Beisha Tang, Chunyu Liu, Chao Chen, Qingtuan Meng
Summary: This study utilized transcriptome-wide association studies and multi-omics analyses to identify the role of PCCB gene in schizophrenia risk through regulating GABAergic pathways.
NATURE COMMUNICATIONS
(2023)
Review
Biochemical Research Methods
Amrutha Hasandka, Ankita Ramchandran Singh, Anusha Prabhu, Hardik Ramesh Singhal, M. S. Giri Nandagopal, Naresh Kumar Mani
Summary: Economic and societal barriers in low-resource areas hinder accessibility to traditional UTI testing methods, while cellulose-based materials offer a portable and adaptable substrate for simple and reproducible UTI diagnosis. Strategies aimed at commercial penetration could significantly increase accessibility to more healthcare options for at-risk populations.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Aaron Tan, Qusai Alsenani, Marcello Lanz, Christopher Birchall, Lauren K. L. Drage, David Picton, Catherine Mowbray, Ased Ali, Christopher Harding, Robert S. Pickard, Judith Hall, Phillip D. Aldridge
Summary: Uropathogenic Escherichia coli is a major cause of urinary tract infections, and flagellin plays a key role in inducing host defenses. Motile isolates from cystitis patients showed uneven distribution patterns, and some of these isolates exhibited a significant increase in NF-kappa B signaling. The NF-kappa B signaling response was not affected by flagellin variability or TLR4 recognition of bacterial lipopolysaccharide. Flagellar abundance was found to be related to the variable host response and may contribute to preventing host TLR5 recognition and bacterial killing.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Physical
Qi Pan, Borui Li, Dong Lin, Ya-Ru Miao, Tao Luo, Tao Yue, Qingming Luo, An-Yuan Guo, Zhihong Zhang
Summary: scLiverDB is a specialized database for human and mouse liver transcriptomes, providing a landscape of liver cell types, cell heterogeneity, and gene expression at single-cell resolution. It has curated 62 datasets, including 9,050 samples and 1,741,734 cells. The database utilizes a uniform workflow for quality control, dimensional reduction, clustering, and cell-type annotation, and offers a user-friendly web interface.
Article
Parasitology
Long Cheng, Sajid Ur Rahman, Hai-Yan Gong, Rong-Sheng Mi, Yan Huang, Yan Zhang, Ju-Liang Qin, Cheng-Cong Yin, Min Qian, Zhao-Guo Chen
Summary: A new mouse model for Toxoplasma pneumonia was established in this study, and transcriptome analysis revealed the molecular mechanisms of the disease. The infected mice showed symptoms such as weight loss, ruffled fur, and respiratory crackles, and lung tissue sections exhibited severe lymphocytic infiltration, pulmonary edema, and typical symptoms of pneumonia. Transcriptome analysis also identified differentially expressed genes associated with the immune system and microbial infections.
PARASITES & VECTORS
(2023)
Article
Microbiology
Rongrong Wu, Ashok Kumar Kumawat, Isak Demirel
Summary: Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC) are common in humans. Trimethylamine N-oxide (TMAO), a proinflammatory metabolite, has been linked to vascular inflammation and chronic kidney disease. This study investigated the effects of TMAO on UTIs and found that it aggravated the release of inflammatory mediators and enhanced UPEC colonization of bladder epithelial cells. These findings suggest a potential role of TMAO in infectious diseases, providing a basis for further research on the link between diet, gut microbiota, and UTIs.
Article
Oncology
Egle Ramelyte, Aizhan Tastanova, Zsolt Balazs, Desislava Ignatova, Patrick Turko, Ulrike Menzel, Emmanuella Guenova, Christian Beisel, Michael Krauthammer, Mitchell Paul Levesque, Reinhard Dummer
Summary: The study found that intralesional T-VEC treatment in primary cutaneous B cell lymphoma patients led to significant tumor response, rapid eradication of malignant cells, activation of the interferon pathway, and early influx of various immune cells, ultimately resulting in enhanced cellular immunity.
Article
Pharmacology & Pharmacy
Isabel Alvarado-Cruz, Mariam Mahmoud, Mohammed Khan, Shilin Zhao, Sebastian Oeck, Rithy Meas, Kaylyn Clairmont, Victoria Quintana, Ying Zhu, Angelo Porciuncula, Hailey Wyatt, Shuangge Ma, Yu Shyr, Yong Kong, Patricia M. LoRusso, Daniel Laverty, Zachary D. Nagel, Kurt A. Schalper, Michael Krauthammer, Joann B. Sweasy
Summary: The study found that long-term treatment with PARP inhibitors induced an inflammatory response in BRCA1 mutant cells, leading to the upregulation of inflammatory genes and activation of the cGAS/STING pathway. In contrast, an increased mutational load was induced in BRCA1-complemented cells treated with a PARP inhibitor.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Ethics
Nikola Biller-Andorno, Andrea Ferrario, Susanne Joebges, Tanja Krones, Federico Massini, Phyllis Barth, Georgios Arampatzis, Michael Krauthammer
Summary: This paper focuses on the ethical questions around the design, development and deployment of AI systems in decision-making processes related to cardiopulmonary resuscitation and code status determination in healthcare. It discusses the challenges in current practices and the openness among healthcare professionals to consider AI-based decision support. The data suggest potential for AI to improve decision-making in resuscitation, with a set of ethically relevant preconditions needing consideration for further development and implementation efforts.
JOURNAL OF MEDICAL ETHICS
(2022)
Article
Biochemical Research Methods
Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez, Michael Krauthammer
Summary: The study introduces a Siamese self-attention multi-modal neural network for predicting drug-drug interactions (DDIs), demonstrating accurate predictions and improved performance, as well as interpretability through an Attention mechanism.
BMC BIOINFORMATICS
(2021)
Article
Microbiology
Ana Montalban-Arques, Egle Katkeviciute, Philipp Busenhart, Anna Bircher, Jakob Wirbel, Georg Zeller, Yasser Morsy, Lubor Borsig, Jesus F. Glaus Garzon, Anne Mueller, Isabelle C. Arnold, Mariela Artola-Boran, Michael Krauthammer, Anna Sintsova, Nicola Zamboni, Gabriel E. Leventhal, Laura Berchtold, Tomas de Wouters, Gerhard Rogler, Katharina Baebler, Marlene Schwarzfischer, Larissa Hering, Ivan Olivares-Rivas, Kirstin Atrott, Claudia Gottier, Silvia Lang, Onur Boyman, Ralph Fritsch, Markus G. Manz, Marianne R. Spalinger, Michael Scharl
Summary: Despite the overall success of T cell checkpoint inhibitors in cancer treatment, research has found that certain commensal species of gut microbiota associated with lower tumor burden and are significantly reduced in CRC patients. Oral application of specific Clostridiales strains can prevent and even treat CRC successfully in mouse models, outperforming anti-PD-1 therapy in some cases. This indicates the potential of gut bacteria as a novel stand-alone therapy against solid tumors.
CELL HOST & MICROBE
(2021)
Article
Medicine, General & Internal
Martina A. Maibach, Ahmed Allam, Matthias P. Hilty, Nicolas A. Perez Gonzalez, Philipp K. Buehler, Pedro D. Wendel Garcia, Silvio D. Brugger, Christoph C. Ganter, Michael Krauthammer, Reto A. Schuepbach, Jan Bartussek
Summary: The study found that aligning patient data using CRP peak values can improve mortality risk stratification in COVID-19 patient cohorts. The data highlights the importance of proper synchronization of longitudinal patient data for accurate interpatient comparisons and relevant subgroup definitions. The use of objective temporal disease markers can facilitate translational research efforts and multicenter trials.
FRONTIERS IN MEDICINE
(2021)
Article
Health Care Sciences & Services
Ahmed Allam, Stefan Feuerriegel, Michael Rebhan, Michael Krauthammer
Summary: Patient trajectories in digital medicine, which record health events over time, can predict the future course of diseases. However, current AI solutions need to adapt to analyze the rich longitudinal data in order to build robust personalized models for risk scoring and disease pathway discovery.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Microbiology
Arwen E. Frick-Cheng, Anna Sintsova, Sara N. Smith, Ali Pirani, Evan S. Snitkin, Harry L. T. Mobley
Summary: More than half of women will experience a urinary tract infection (UTI), with uropathogenic Escherichia coli (UPEC) causing the majority of cases. Iron acquisition systems play a crucial role in UPEC pathogenesis, and this study reveals the importance of the ferric citrate uptake system as an alternative iron source when other siderophores are limited. Understanding these iron acquisition mechanisms is important for developing new strategies to combat UTI.
Article
Medicine, General & Internal
Uwe Bieri, Michael Scharl, Silvan Sigg, Barbara Maria Szczerba, Yasser Morsy, Jan Hendrik Ruschoff, Peter Hans Schraml, Michael Krauthammer, Lukas John Hefermehl, Daniel Eberli, Cedric Poyet
Summary: The human microbiota has been linked to inflammatory and neoplastic diseases. While the gut microbiome has been extensively studied, the urinary microbiome is still relatively new. Investigating the relationship between bladder cancer and the bladder and intestinal microbiome may provide insights into their pathophysiological relationship. It may also lead to the discovery of non-invasive biomarkers for tumor behavior.
Article
Biology
Gaetana Restivo, Aizhan Tastanova, Zsolt Balazs, Federica Panebianco, Maren Diepenbruck, Caner Ercan, Bodgan-T Preca, Juerg Hafner, Walter P. Weber, Christian Kurzeder, Marcus Vetter, Simone Munst Soysal, Christian Beisel, Mohamed Bentires-Alj, Salvatore Piscuoglio, Michael Krauthammer, Mitchell P. Levesque
Summary: Fresh and slow-frozen tissues from various malignancies are comparable and suitable for different methods, including culture establishment and RNA sequencing, with similar results to freshly analyzed material.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Nicolas Mathis, Ahmed Allam, Lucas Kissling, Kim Fabiano Marquart, Lukas Schmidheini, Cristina Solari, Zsolt Balazs, Michael Krauthammer, Gerald Schwank
Summary: This study conducted a high-throughput screen to identify sequence context features that influence prime editing outcomes. They trained a neural network called PRIDICT, which reliably predicts editing rates for various genetic changes. The validation results showed that PRIDICT can significantly increase prime editing efficiencies in different cell types.
NATURE BIOTECHNOLOGY
(2023)
Article
Rheumatology
Alexandru Garaiman, Farhad Nooralahzadeh, Carina Mihai, Nicolas Perez Gonzalez, Nikitas Gkikopoulos, Mike Oliver Becker, Oliver Distler, Michael Krauthammer, Britta Maurer
Summary: The study aims to evaluate the performance of a vision transformer-based deep-learning model in identifying microangiopathy in NFC images of SSc patients and compare it with the performance of rheumatologists. The results show that the ViT performs well in identifying different microangiopathic changes, but there is still room for improvement in terms of reliability compared to rheumatologists.
Article
Microbiology
A. E. Shea, A. E. Frick-Cheng, S. N. Smith, H. L. T. Mobley
Summary: This study demonstrates that phenotypic characteristics can be used to predict the severity of urinary tract infection caused by uropathogenic Escherichia coli (UPEC) strains. These characteristics can help differentiate UPEC from other E. coli strains and reduce the overuse of antibiotics.
Article
Ethics
Jeffrey David Iqbal, Michael Krauthammer, Nikola Biller-Andorno
Summary: This paper introduces the concept and use cases of digital twins in medicine, discusses ethical challenges, and explores their impact on future medical practice.
JOURNAL OF LAW MEDICINE & ETHICS
(2022)
Article
Biochemical Research Methods
Aizhan Tastanova, Egle Ramelyte, Zsolt Balazs, Ulrike Menzel, Christian Beisel, Michael Krauthammer, Reinhard Dummer, Mitchell Paul Levesque
Summary: High cell viability and recovered cell concentration are crucial for quality control in single-cell processing and data analysis. This protocol details procedures for sampling, preprocessing, and analyzing fine-needle aspiration (FNA) samples of the skin, which is minimally invasive and allows for longitudinal sampling to capture cellular heterogeneity in clinical samples.