Article
Engineering, Biomedical
Jaehwan Ahn, Jun-Ho Ahn, Seokjoo Yoon, Mi-Young Son, Sungbo Cho, Jung-Hwa Oh
Summary: The study developed impedance assessment systems to quantify NAFLD progression in 3D liver microtissue, showing good representation of clinical characteristics of various stages. Bioimpedance simulation revealed a correlation between impedance parameters and pathophysiological characteristics of NAFLD progression, while a method for assessing fibrogenesis relative stiffness was identified through resistance change and elongation length correlation in smaller microchannels of hMTs.
Editorial Material
Biochemical Research Methods
Ludvig Larsson, Jonas Frisen, Joakim Lundeberg
Summary: Spatially resolved transcriptomics is a field that has emerged with the advancement of single-cell omics, utilizing experimental and computational methods to map out cell positions and gene expression profiles in space. Current methodologies and applications in genomics research are summarized in this field.
Editorial Material
Biochemical Research Methods
Xiaowei Zhuang
Summary: The recent development of genome-scale imaging allows for single-cell omics analysis in intact cells and tissues, enabling gene expression profiling, identification of cell types, and spatial mapping in complex tissues. The high spatial resolution of these approaches also allows for determining the spatial organizations of the genome and transcriptome inside cells, which are key regulatory mechanisms for gene expression.
Article
Microbiology
Roel Tans, Shoumit Dey, Nidhi Sharma Dey, Grant Calder, Peter O'Toole, Paul M. Kaye, Ron M. A. Heeren
Summary: Infectious diseases often lead to focal inflammation in distinct tissues, with different tissue-specific outcomes. Spatially resolved multi-omics analysis, including molecular imaging techniques, can identify metabolic signatures in inflammatory microenvironments and aid in understanding disease pathogenesis and potential therapeutic targets.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Gastroenterology & Hepatology
Ping Lin, Xi Yan, Siyu Jing, Yanhong Wu, Yiran Shan, Wenbo Guo, Jin Gu, Yu Li, Haibing Zhang, Hong Li
Summary: Single-cell transcriptomics and spatially resolved transcriptomics can identify rare cell types and infer state transitions, enabling quantitative analysis of cells and genes in tissues. The advancements in these technologies are enhancing our understanding of the cellular landscape and its role in diseases.
Article
Chemistry, Analytical
Lauranne Drelich, Soulaimane Aboulouard, Julien Franck, Michel Salzet, Isabelle Fournier, Maxence Wisztorski
Summary: Expansion microscopy is a novel method that allows morphological examination of biological specimens at nanoscale resolution through physical tissue expansion; this approach can be used for large-scale proteomics research by enlarging tissues several fold.
ANALYTICAL CHEMISTRY
(2021)
Review
Gastroenterology & Hepatology
Eunyoung Lee, Hannelie Korf, Antonio Vidal-Puig
Summary: The liver and white adipose tissue play critical roles in regulating systemic energy balance. While they can adapt to energy surplus to a certain extent, excessive accumulation of fat in adipose tissue can lead to metabolic disturbances and inflammation. This can result in liver overload and the development of diseases such as non-alcoholic fatty liver.
JOURNAL OF HEPATOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Bingbing Liu, Xiaoxiao Wang, Kun Li, Zongwei Cai
Summary: This study utilized metabolomics, lipidomics, and mass spectrometry imaging to investigate the spatial distribution of different metabolites and lipids in two cottonseed cultivars under drought and salt stress. The findings highlighted the potential roles of these substances in enhancing stress tolerance and provided insights into metabolic and lipidomic regulatory networks in coping with salinity and drought stresses.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Xiang Gao, Valerij G. Kiselev, Thomas Lange, Juergen Hennig, Maxim Zaitsev
Summary: An open-source spatially resolved phase graph framework is proposed for simulating arbitrary pulse sequences efficiently in three dimensions and estimating signal modulation. The framework's effectiveness is validated through several application examples showing its ability to analyze signal evolution in both frequency and spatial domain.
MAGNETIC RESONANCE IN MEDICINE
(2021)
Review
Biochemical Research Methods
Vilmos Kertesz, John F. Cahill
Summary: Mass spectrometry has become the primary tool for routine quantitative analysis of biomolecules, and is increasingly used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue. However, most spatially resolved MS measurements are qualitative due to potential biases. As demand for quantitative MS imaging and profiling data increases in pharmacological and clinical fields, various technologies now exist to provide different levels of spatial and quantitative information.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Immunology
Lindsay T. Fourman, Takara L. Stanley, Isabel Zheng, Chelsea S. Pan, Meghan N. Feldpausch, Julia Purdy, Julia Aepfelbacher, Colleen Buckless, Andrew Tsao, Kathleen E. Corey, Raymond T. Chung, Martin Torriani, David E. Kleiner, Colleen M. Hadigan, Steven K. Grinspoon
Summary: This study observed high rates of hepatic fibrosis and progression in patients with HIV-associated NAFLD. Visceral adiposity was identified as a novel predictor of worsening fibrosis. Baseline histologic characteristics did not relate to fibrosis progression.
CLINICAL INFECTIOUS DISEASES
(2021)
Review
Medicine, Research & Experimental
Lijun Luo, Yongchun Chang, Li Sheng
Summary: Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease worldwide, but its pathogenesis is still unclear. Recent research has shown a close relationship between the intestinal microbiome and NAFLD, and the theory of the gut-liver axis has been proposed. This review focuses on the role of gut bacteria and their components and metabolites in the progression of NAFLD, providing important insights into the pathogenesis, diagnosis, and treatment of this prevalent liver disease.
Article
Cell Biology
Chiara D'Ercole, Paolo D'Angelo, Veronica Ruggieri, Daisy Proietti, Laura Virtanen, Cristina Parisi, Carles Sanchez Riera, Alessandra Renzini, Alberto Macone, Marta Marzullo, Laura Ciapponi, Davide Bonvissuto, Claudio Sette, Lorenzo Giordani, Luca Madaro
Summary: The study utilizes spatially resolved transcriptomics and immunofluorescence to explore the relationship between muscle structure and gene expression and discovers the response to external perturbations. The study also investigates the changes in the transcriptome of specific domains in a denervation model and identifies the impact of polyamine metabolism on muscle function.
Article
Neurosciences
Wesley Wang, Jonah Domingo Tugaoen, Paolo Fadda, Amanda Ewart Toland, Qin Ma, J. Brad Elder, Pierre Giglio, Jose Javier Otero
Summary: The levels of cancer-immune cell activity correlate with heterogeneous clinical outcomes in patients with glioblastoma. The gene expression pathways of pseudoprogression are dominated by immune activation, while progression is predominated by cell cycle activity.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Holly-May Lewis, Catia Costa, Veronique Dartois, Firat Kaya, Mark Chambers, Janella de Jesus, Vladimir Palitsin, Roger Webb, Melanie J. Bailey
Summary: This study combines elemental imaging and a new method for spatially resolved lipidomics to investigate the relationship between metals, drugs, and lipids in different areas of tissues. The method was applied to rabbit lung tissues with tuberculosis infection and demonstrated the association between ion accumulation, lipid profiles, and local drug distribution.
ANALYTICAL CHEMISTRY
(2022)
Article
Gastroenterology & Hepatology
Huy Duc Le, Theresa Pflaum, Johannes Labrenz, Soner Sari, Fabienne Bretschneider, Florian Tran, Arne Lassen, Susanna Nikolaus, Silke Szymczak, Diana Kormilez, Philip Rosenstiel, Stefan Schreiber, Konrad Aden, Christoph Roecken
Summary: This study evaluated histological disease activity in UC patients and found that the Nancy index is a reliable measure. However, there was poor agreement in the assessment of NI grade 1. It is important to specify histological characteristics leading to NI grade 1.
JOURNAL OF CROHNS & COLITIS
(2023)
Article
Oncology
Magnus Kock Am Brink, Laura Sophie Dunst, Hans-Michael Behrens, Sandra Krueger, Thomas Becker, Christoph Roecken
Summary: The study investigates the problem of intratumoral heterogeneity (ITH) in gastric cancer (GC), and tests the effects of Ki67 and tumor regression on ITH after neoadjuvant/perioperative chemotherapy. The results suggest that Ki67 is significantly associated with tumor regression and may serve as a predictor for chemotherapy sensitivity and an indicator of ITH.
BRITISH JOURNAL OF CANCER
(2023)
Article
Cell Biology
Maarten P. Bebelman, Matthew J. Bovyn, Carlotta M. Mayer, Julien Delpierre, Ronald Naumann, Nuno P. Martins, Alf Honigmann, Yannis Kalaidzidis, Pierre A. Haas, Marino Zerial
Summary: Bebelman and Bovyn et al. demonstrate that apical bulkheads are load-bearing mechanical elements that contribute to the ability of bile canaliculi to withstand elevated luminal pressure. Through their structure and function analysis, they found that apical bulkheads are sealed by tight junction loops, connected by adherens junctions, and contain contractile actomyosin. The study also revealed that apical bulkheads can double the pressure bile canaliculi can hold and protect the bile duct network against elevated pressure.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Claudia Geismann, Charlotte Hauser, Frauke Grohmann, Christian Schneeweis, Nico Boelter, Jan-Paul Gundlach, Gunter Schneider, Christoph Roecken, Christian Meinhardt, Heiner Schaefer, Stefan Schreiber, Alexander Arlt
Summary: The resistance to systemic therapies in PDAC remains a major challenge in clinical practice, and NF-kappa B activity plays a crucial role in this process. A20, identified as an NF-kappa B target gene, is associated with elevated RelA expression in PDAC patients. Elevated A20 expression leads to resistance to TRAIL-induced apoptosis but not to chemotherapeutic-induced cell death, mediated by its E3-ligase activity-mediating Zink finger domain. Additionally, p62 is found to be indispensable for the TRAIL-mediated apoptosis-inducing pathway affected by A20.
CELL DEATH & DISEASE
(2023)
Article
Oncology
Michaela Kuhlen, Marina Kunstreich, Stefan A. Wudy, Paul-Martin Holterhus, Lienhard Lessel, Dominik T. Schneider, Ines B. Brecht, Denis M. Schewe, Guido Seitz, Christoph Roecken, Christian Vokuhl, Pascal D. Johann, Michael C. Fruehwald, Peter Vorwerk, Antje Redlich
Summary: This study analyzes the clinical characteristics and prognosis of 161 pediatric ACT patients. The findings indicate that age, initial biopsy, tumor spillage, incomplete tumor resection, and unfavorable histology are associated with overall survival and event-free survival.
Letter
Biochemistry & Molecular Biology
J. C. Purrucker, C. Roecken, D. Reuss
AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
(2023)
Article
Biochemistry & Molecular Biology
Christian Treitz, Neelis Mueller-Marienburg, Rolf Ruediger Meliss, Peter Urban, Hans-Detlef Axmann, Frank Siebert, Karsten Becker, Klaus Martens, Hans-Michael Behrens, Eva Gericke, Andreas Tholey, Christoph Roecken
Summary: This study found unclassifiable amyloid deposits in the annular ligament during surgical treatment of trigger finger. Using comprehensive analysis methods, it was determined that there are two different types of amyloid affecting the annular ligament, ATTR amyloid and AFib amyloid, with distinct patient characteristics and deposition patterns. The unknown amyloid was identified as most likely of fibrinogen origin.
AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
(2023)
Article
Oncology
Wiebke Siemsen, Christine Halske, Hans-Michael Behrens, Sandra Krueger, Christoph Becker-Pauly, Christoph Roecken
Summary: In this study, the expression of meprin beta in gastric cancer was found to be differentially regulated and correlated with clinicopathological characteristics and patient survival. It may function as either a tumor suppressor or promotor depending on the histological site and context.
Article
Oncology
Dita Ulase, Hans-Michael Behrens, Sandra Krueger, Steffen M. Heckl, Ulrike Ebert, Thomas Becker, Christoph Roecken
Summary: This study analyzed the spatial distribution of LAG3 + cells in gastric cancer and its correlation with clinicopathological and survival data. The results demonstrated significant differences in the spatial distribution of LAG3 + cells and their association with prognosis. The findings highlight the importance of LAG3 as a potential prognostic factor and suggest its role in clinical outcomes and treatment responses.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Biochemical Research Methods
Daniel Capek, Matvey Safroshkin, Hernan Morales-Navarrete, Nikan Toulany, Grigory Arutyunov, Anica Kurzbach, Johanna Bihler, Julia Hagauer, Sebastian Kick, Felicity Jones, Ben Jordan, Patrick Mueller
Summary: This study uses machine learning to develop a deep convolutional neural network, EmbryoNet, for automated phenotyping of zebrafish signaling mutants. This network accurately identifies and classifies phenotypic defects caused by loss of function in major signaling pathways relevant for vertebrate development. The classification algorithms have wide applications in developmental biology and can identify signaling defects in evolutionarily distant species. Additionally, EmbryoNet can be used for mechanism of action determination in high-throughput drug screens.
Article
Clinical Neurology
Hajrullah Ahmeti, Amke Caliebe, Nourane Trigui, Ilay Alati, Christoph Roecken, Olav Jansen, Michael Synowitz, Maximilian H. Mehdorn
Summary: A systematic investigation of 210 patients with convexity meningiomas revealed that large tumor volume and brain infiltration were significant factors for postoperative complications. The clinical conditions of patients significantly improved postoperatively and further during the follow-up period.
CLINICAL NEUROLOGY AND NEUROSURGERY
(2023)
Article
Biochemistry & Molecular Biology
Carlotta Mayer, Sophie Nehring, Michael Kuecken, Urska Repnik, Sarah Seifert, Aleksandra Sljukic, Julien Delpierre, Hernan Morales-Navarrete, Sebastian Hinz, Mario Brosch, Brian Chung, Tom Karlsen, Meritxell Huch, Yannis Kalaidzidis, Lutz Brusch, Jochen Hampe, Clemens Schafmayer, Marino Zerial
Summary: Hepatocytes dynamically respond to bile acids and bile flow, but little is known about their response to intraluminal pressure. This study reveals that hepatocytes form apical bulkheads in response to obstructed bile flow, which protect bile canaliculi against elevated pressure. The loss of apical bulkheads leads to abnormally dilated canaliculi, highlighting the importance of canalicular pressure in liver diseases.
Article
Biochemistry & Molecular Biology
Florian Richter, Clara Henssen, Tim Alexander Steiert, Tobias Meissner, Anne-Sophie Mehdorn, Christoph Roecken, Andre Franke, Jan-Hendrik Egberts, Thomas Becker, Susanne Sebens, Michael Forster
Summary: Esophageal cancer (EC) has a high mortality rate, and optimizing therapies and dynamically adapting to individuals is crucial. Liquid biopsy is an increasingly important method for residual disease monitoring, but conflicting detection rates and varying levels of circulating tumor DNA (ctDNA) have been observed in previous studies. This study aims to resolve this discrepancy and found that ctDNA in blood can be used for therapy monitoring of EC patients. A combination of solid and liquid samples should be used to guide individualized EC therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Mathematics, Interdisciplinary Applications
Robert Mueller, Arthur Boutillon, Diego Jahn, Joern Starruss, Nicolas B. David, Lutz Brusch
Summary: Collective cell migration is a crucial process in biological development and tissue repair, but it can become malignant during tumor invasion. Mathematical and computational models are essential for understanding the self-organization mechanisms that drive collective migration from individual cell interactions. This study explores how guidance stimuli are integrated when multiple cells interact simultaneously, using an individual-based model. The results show that collective cell migration remains robust and qualitatively the same regardless of the variant of stimulus integration considered. This study highlights the importance of individual-based modeling for understanding collective phenomena arising from cell-cell interactions.
FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS
(2023)
