Article
Biochemistry & Molecular Biology
Eleanna Kaffe, Manolis Roulis, Jun Zhao, Rihao Qu, Esen Sefik, Haris Mirza, Jing Zhou, Yunjiang Zheng, Georgia Charkoftaki, Vasilis Vasiliou, Daniel F. Vatner, Yuval Kluger, Richard A. Flavell
Summary: Metabolic functions of hepatocytes are regulated by non-parenchymal cells in their microenvironment, revealing the importance of microenvironmental regulation in liver metabolism.
Review
Oncology
Alba Loras, Cristina Segovia, Jose Luis Ruiz-Cerda
Summary: Current diagnostic and follow-up methods for bladder cancer have limitations and there is a need for non-invasive biomarkers. Personalized treatments can improve patient quality of life and overall survival. The interplay between epigenetics and metabolism is closely linked to tumor phenotype, providing valuable insights for researchers and clinical decision-making in the field of bladder cancer.
Article
Multidisciplinary Sciences
Nikolas L. Jorstad, Jennie Close, Nelson Johansen, Anna Marie Yanny, Eliza R. Barkan, Kyle J. Travaglini, Darren Bertagnolli, Jazmin Campos, Tamara Casper, Kirsten Crichton, Nick Dee, Song-Lin Ding, Emily Gelfand, Jeff Goldy, Daniel Hirschstein, Katelyn Kiick, Matthew Kroll, Michael Kunst, Kanan Lathia, Brian Long, Naomi Martin, Delissa Mcmillen, Trangthanh Pham, Christine Rimorin, Augustin Ruiz, Nadiya Shapovalova, Soraya Shehata, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Edward M. Callaway, Patrick R. Hof, C. Dirk Keene, Boaz P. Levi, Sten Linnarsson, Partha P. Mitra, Kimberly Smith, Rebecca D. Hodge, Trygve E. Bakken, Ed S. Lein
Summary: The cellular structure and specialization of distinct cortical areas vary across the human neocortex, and can be quantitatively compared using single-nucleus and spatial transcriptomic methods.
Article
Biotechnology & Applied Microbiology
Maciej Migdal, Eugeniusz Tralle, Karim Abu Nahia, Lukasz Bugajski, Katarzyna Zofia Kedzierska, Filip Garbicz, Katarzyna Piwocka, Cecilia Lanny Winata, Michal Pawlak
Summary: Our study induced hepatic injury in adult zebrafish using thioacetamide (TAA). We isolated three major liver cell types - hepatocytes, endothelial cells, and hepatic stellate cells - and identified cell-type-specific chromatin accessibility and transcriptional changes in the early stage of liver injury. The results showed that TAA induced transcriptional shifts in all three cell types, with liver endothelial cells exhibiting the most pronounced response to liver injury at the transcriptome and chromatin level.
Article
Biochemistry & Molecular Biology
Xushen Xiong, Benjamin T. James, Carles A. Boix, Yongjin P. Park, Kyriaki Galani, Matheus B. Victor, Na Sun, Lei Hou, Li-Lun Ho, Julio Mantero, Aine Ni Scannail, Vishnu Dileep, Weixiu Dong, Hansruedi Mathys, David A. Bennett, Li-Huei Tsai, Manolis Kellis
Summary: This study examines the epigenomic and transcriptional features of brain cells to understand the regulatory circuits and mechanisms of Alzheimer's disease (AD). The findings reveal the enrichment of AD risk loci in microglial enhancers and the differential accessibility of regulatory modules in late-stage AD brains, suggesting global epigenome dysregulation and cell identity loss in AD.
Article
Genetics & Heredity
Chiara Anania, Rafael D. Acemel, Johanna Jedamzick, Adriano Bolondi, Giulia Cova, Norbert Brieske, Ralf Kuehn, Lars Wittler, Francisca M. Real, Dario G. Lupianez
Summary: This study investigates the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vertebrate genomes and highlights their modular nature and importance in developmental processes.
Article
Biotechnology & Applied Microbiology
Harindra E. Amarasinghe, Ping Zhang, Justin P. Whalley, Alice Allcock, Gabriele Migliorini, Andrew C. Brown, Giuseppe Scozzafava, Julian C. Knight
Summary: This study investigates the epigenetic regulation in monocytes during innate immune activation, including acute response and endotoxin tolerance states. Differential gene expression, chromatin accessibility, and enhancer-derived RNA signatures were identified, with distinct patterns in endotoxin tolerance models. Integrating eQTL mapping and GWAS analysis revealed potential therapeutic targets for immunosuppression and diseases.
Article
Virology
Xi Zeng, Yuyouye Wang, Binghan Liu, Xinjie Rao, Canhui Cao, Fang Peng, Wenhua Zhi, Ping Wu, Ting Peng, Ye Wei, Tian Chu, Miaochun Xu, Yashi Xu, Wencheng Ding, Guoliang Li, Shitong Lin, Peng Wu
Summary: Integration of human papilloma virus (HPV) DNA into the human genome may progressively contribute to cervical carcinogenesis. We analyzed multiomics data from 50 patients with cervical cancer to explore how HPV integration affects gene expression by altering DNA methylation. High-frequency HPV-integrated genes, including five novel recurrent genes, were identified. HPV integrations occurring in exons were associated with altered gene expression in tumor tissues. Our study provides novel insights into HPV-induced cervical cancer at the biological and clinical level.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bing Wang, Boyan Zhang, Lin Zhou, Shuanghong Li, Zhen Li, Hailing Luo
Summary: Using multi-omics approaches, we investigated the molecular mechanism underlying diet-induced metabolic liver disorders through the microbiota-gut-liver axis. The analysis of metataxonomics, metaproteomics, transcriptomics, and metabolomics revealed the microbial mechanisms related to metabolic disorders and liver injury. The high-energy diet led to hepatic inflammation, reduced antimicrobial and antioxidant functions of the rumen microbiome, and activated proinflammatory cytokines. Integrated multi-omics analyses demonstrated interactions among the rumen and jejunum microbiota, circulating metabolites, and liver gene expression, suggesting a systemic immune response and liver disorder mediated by the microbiota-gut-liver axis.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Ben Stocks, Alba Gonzalez-Franquesa, Melissa L. Borg, Marie Bjornholm, Lili Niu, Juleen R. Zierath, Atul S. Deshmukh
Summary: This study investigates the changes in the liver and plasma proteome associated with obesity using ob/ob mice as a model. It identifies proteins that are concomitantly regulated in the liver and plasma in obesity, suggesting a liver-plasma cross talk. The findings have clinical importance as many of these proteins are also regulated during type 2 diabetes and/or NAFLD in humans.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Carolina M. Greco, Kevin B. Koronowski, Jacob G. Smith, Jiejun Shi, Paolo Kunderfranco, Roberta Carriero, Siwei Chen, Muntaha Samad, Patrick-Simon Welz, Valentina M. Zinna, Thomas Mortimer, Sung Kook Chun, Kohei Shimaji, Tomoki Sato, Paul Petrus, Arun Kumar, Mireia Vaca-Dempere, Oleg Deryagian, Cassandra Van, Jose Manuel Monroy Kuhn, Dominik Lutter, Marcus M. Seldin, Selma Masri, Wei Li, Pierre Baldi, Kenneth A. Dyar, Pura Munoz-Canoves, Salvador Aznar Benitah, Paolo Sassone-Corsi
Summary: The study investigated the interaction between feeding and the liver clock by reconstituting Bmal1 in hepatocytes, finding that BMAL1 and CEBPB cooperate to regulate daily liver metabolic transcriptional programs. The liver clock and feeding rhythm are sufficient to drive temporal carbohydrate homeostasis, while liver rhythms tied to redox and lipid metabolism require communication with the skeletal muscle clock, highlighting peripheral clock cross-talk.
Article
Biology
Ngozi D. Akingbesote, Brooks P. Leitner, Daniel G. Jovin, Reina Desrouleaux, Dennis Owusu, Wanling Zhu, Zongyu Li, Michael N. Pollak, Rachel J. Perry
Summary: This study investigates metabolic scaling from multiple perspectives and finds that it is not only related to oxygen consumption, but also to other metabolic processes. It is regulated at the level of gene and protein expression, enzyme activity, and substrate supply.
Article
Multidisciplinary Sciences
Marielle J. F. M. van Kooten, Clio A. Scheidegger, Matthias Christen, Beat Christen
Summary: Rewriting genomes allows for complete annotation of gene regulatory elements. Here the authors compare endogenous and rewritten segments of a genome and find extensive transcriptional changes, based on which they formulate design principles that aid in the programming of biological systems.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sanchari Bhattacharyya, Shimon Bershtein, Bharat Adkar, Jaie Woodard, Eugene Shakhnovich
Summary: This study reveals that partial loss of DHFR activity in E. coli strains leads to filamentous growth due to a disproportionate drop in intracellular dTTP levels, which is influenced by highly cooperative activity of Tmk. Supplementing dTMP can rescue filamentation and restore normal in vivo Tmk kinetics.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Chemistry, Analytical
Fangying Shi, Chuwen Huang, Yuan Ren, Chunhui Deng, Nianrong Sun, Xizhong Shen
Summary: We designed a mesoporous superstructure with silicon atom-doped nanowire arrays uniformly loaded with Pt nanoparticles to efficiently extract high-quality metabolic fingerprints from only 35 nL of serum within seconds. Using machine learning algorithms, we established specific biomarker panels to distinguish different liver diseases with over 90% accuracy and identified key metabolites for discrimination with 100% sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Clinical Neurology
Hajrullah Ahmeti, Eva Juettner, Christoph Roecken, Olav Jansen, Matthias Laudes, Michael Synowitz
Summary: Pituitary gland metastases are rare and often diagnosed during autopsies. The most common primary tumors that metastasize to the pituitary gland are breast, lung, thyroid, and renal carcinomas. We present a rare case of spindle cell rhabdomyosarcoma metastasizing to the pituitary gland. The patient experienced symptoms such as headache, visual disorder, panhypopituitarism, and diabetes insipidus. Despite the inability to surgically remove the tumor, biopsy confirmed the diagnosis and the patient received chemotherapy and irradiation. Even high-risk patients can achieve remission after treatment.
JOURNAL OF NEUROLOGICAL SURGERY PART A-CENTRAL EUROPEAN NEUROSURGERY
(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
Clinical Neurology
Ulf Jensen-Kondering, Nils G. Margraf, Caroline Weiler, Walter Maetzler, Justina Dargvainiene, Kim Falk, Sarah Philippen, Thorsten Bartsch, Charlotte Flueh, Christoph Roecken, Bettina Moeller, Georg Royl, Alexander Neumann, Norbert Brueggemann, Benjamin Roeben, Claudia Schulte, Benjamin Bender, Daniela Berg, Gregor Kuhlenbaeumer
Summary: This study compared the clinical, radiological, and cerebrospinal fluid marker data of patients with CAA, MLH, AD, and healthy controls. The results showed that cSS was more common in CAA, and MLH with cSS was associated with ICH. The concentrations of cerebrospinal fluid markers differed among the groups.
INTERNATIONAL JOURNAL OF STROKE
(2023)
Correction
Immunology
Natalie Katzmarski, Jorge Dominguez-Andres, Branko Cirovic, Georgios Renieris, Eleonora Ciarlo, Didier Le Roy, Konstantin Lepikhov, Kathrin Kattler, Gilles Gasparoni, Kristian Haendler, Heidi Theis, Marc Beyer, Jos W. M. van der Meer, Leo A. B. Joosten, Joern Walter, Joachim L. Schultze, Thierry Roger, Evangelos J. Giamarellos-Bourboulis, Andreas Schlitzer, Mihai G. Netea
Article
Endocrinology & Metabolism
Manuel Gado, Annett Heinrich, Denise Wiedersich, Katrin Sameith, Andreas Dahl, Vasileia I. Alexaki, Michael M. Swarbrick, Ulrike Baschant, Ingo Grafe, Nikolaos Perakakis, Stefan R. Bornstein, Martina Rauner, Lorenz C. Hofbauer, Holger Henneicke
Summary: This study demonstrates that activation of the sympathetic nervous system through cold exposure or selective I33-adrenergic receptor agonist can alleviate the adverse metabolic effects caused by chronic glucocorticoid exposure. Cold exposure preserves the function of brown adipose tissue and reverses white adipose tissue lipid accumulation, correcting obesity, hyperinsulinemia, and hyperglycemia caused by glucocorticoids.
AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM
(2023)
Article
Biochemistry & Molecular Biology
Sharanya Bola, Pallavi Subramanian, Daniela Calzia, Andreas Dahl, Isabella Panfoli, Richard H. W. Funk, Cora Roehlecke
Summary: We conducted a detailed analysis of cellular events in blue light stressed 661W cells that were subjected to direct current electric field (EF) stimulation. Our findings revealed that EF stimulation can protect cells from blue light-induced stress through various defense mechanisms, including increased mitochondrial activity, elevated mitochondrial potential, increased superoxide levels, and activation of the unfolded protein response (UPR) pathways. Our genetic screen results suggest that UPR pathway can be a potential therapeutic target for alleviating blue light-induced stress through EF stimulation. Hence, our study is significant for the clinical application of EF stimulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Biochemistry & Molecular Biology
Tim A. Steiert, Genis Parra, Marta Gut, Norbert Arnold, Jean-Remi Trotta, Raul Tonda, Alice Moussy, Zuzana Gerber, Peter M. Abuja, Kurt Zatloukal, Christoph Roecken, Trine Folseraas, Marit M. Grimsrud, Arndt Vogel, Benjamin Goeppert, Stephanie Roessler, Sebastian Hinz, Clemens Schafmayer, Philip Rosenstiel, Jean-Francois Deleuze, Ivo G. Gut, Andre Franke, Michael Forster
Summary: Formalin fixation with paraffin-embedding (FFPE) was developed in the late 19th century and is still commonly used in clinical practice. However, FFPE samples can undergo DNA damage, leading to potential errors in sequencing and analysis. This review discusses mitigation strategies in sample quality control, DNA repair treatments, sample preparation, and bioinformatic analysis of FFPE-DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Diana Ezhkova, Simone Schwarzer, Sandra Spiess, Michaela Geffarth, Anja Machate, Daniela Zoeller, Johanna Stucke, Dimitra Alexopoulou, Mathias Lesche, Andreas Dahl, Stefan Hans
Summary: The vertebrate inner ear, which is responsible for hearing and balance, develops from the otic placode and is regulated by the distal-less homeodomain transcription factors Dlx3b/4b. Transcriptome analysis revealed numerous genes regulated by Dlx3b/4b, which are important for otic development. These findings provide valuable insights into the gene regulatory network and molecular control of inner ear formation, which may have implications for treating hearing loss in humans.
Editorial Material
Toxicology
Klaus-Michael Wollin, Monika Batke, Georg Damm, Alexius Freyberger, Ursula Gundert-Remy, Aswin Mangerich, Jan G. Hengstler, Falko Partosch, Thomas Schupp, Anna Sonnenburg, Heidi Foth
Summary: PFASs are substances that contain fully fluorinated methyl or methylene carbon atoms. They have excellent technical properties and are used in various applications. There are over 10,000 compounds in this group, but data on their toxicokinetics and effects is lacking for most of them. The high persistence of PFASs and their degradation products poses a problem, and the European Commission plans to take action. However, closing the data gaps would take a long time, and the precautionary principle has been chosen as a suitable approach. Communication about PFASs has led to misunderstandings, and it should clarify the justification for the broad inclusion of substances based on the precautionary principle, communicate data gaps and current knowledge, mention the possibility of derogation for essential use, discuss suitable substitutes to avoid unintended health consequences, and emphasize the need for innovation in remediation techniques to address persistent environmental contamination.
ARCHIVES OF TOXICOLOGY
(2023)
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
Pathology
Samir Abdullazade, Hans-Michael Behrens, Sandra Krueger, Jochen Haag, Christoph Roecken
Summary: The study validated gene amplification, protein expression, and tumor biological function of MDM2 in gastric cancer, and found a significant correlation between MDM2 amplification and protein expression. However, MDM2 amplification and expression were not associated with patient survival.
Article
Multidisciplinary Sciences
Anke Witt, Ivona Mateska, Alessandra Palladini, Anupam Sinha, Michele Woelk, Akiko Harauma, Nicole Bechmann, Christina Pamporaki, Andreas Dahl, Michael Rothe, Irakli Kopaliani, Christian Adolf, Anna Riester, Ben Wielockx, Stefan R. Bornstein, Matthias Kroiss, Mirko Peitzsch, Toru Moriguchi, Maria Fedorova, Michal Grzybek, Triantafyllos Chavakis, Peter Mirtschink, Vasileia Ismini Alexaki
Summary: Corticosteroids play a crucial role in regulating various physiological processes, and their production is influenced by the polyunsaturated fatty acid (PUFA) content in mitochondrial phospholipids in adrenocortical cells. Inhibition of the enzyme FADS2, which is involved in PUFA synthesis, disrupts mitochondrial lipid composition and reduces steroidogenesis. FADS2 expression is elevated in obese mice, leading to increased corticosterone levels, but this can be countered by using FADS2 inhibitors or PUFA supplementation. Furthermore, FADS2 expression is elevated in aldosterone-producing adenomas in humans, indicating its role in adrenal steroidogenesis in health and disease.
Article
Geriatrics & Gerontology
Patricia Huebbe, Stephanie Bilke, Johanna Rueter, Anke Schloesser, Graeme Campbel, Claus-C. Glueer, Ralph Lucius, Christoph Roecken, Andreas Tholey, Gerald Rimbach
Summary: Recent studies have found that the human APOE epsilon 4 allele protects against non-alcoholic fatty liver disease (NAFLD), while epsilon 3 promotes hepatic steatosis and steatohepatitis. In this study, mice expressing the APOE3 or APOE4 protein isoforms were fed a high-fat and high-sucrose diet to induce obesity. The results showed that APOE3 mice had higher liver weights and exhibited more severe hepatic steatosis compared to APOE4 mice. Proteome analysis also revealed differences in proteins related to inflammation, damage response, and lipid storage between APOE3 and APOE4 mice. These findings support the association of increased NAFLD risk with the APOE epsilon 3 allele and suggest potential mechanisms of protection conferred by APOE epsilon 4.
Article
Medicine, Research & Experimental
Hajrullah Ahmeti, Amke Caliebe, Christoph Rocken, Olav Jansen, Maximilian H. Mehdorn, Michael Synowitz
Summary: This study systematically examined 696 patients with primary intracranial meningiomas to assess the effect of preoperative peritumoral brain edema (PTBE) on preoperative symptoms, neurological deficits, postoperative complications, and long-term outcomes. Results showed that PTBE significantly increased the incidences of specific preoperative symptoms, neurological deficits, and postoperative complications. Patients with preoperative PTBE required more medical support after surgery, but all patients had favorable outcomes.
EUROPEAN JOURNAL OF MEDICAL RESEARCH
(2023)