Review
Medicine, General & Internal
Isa Mambetsariev, Jeremy Fricke, Stephen B. Gruber, Tingting Tan, Razmig Babikian, Pauline Kim, Priya Vishnubhotla, Jianjun Chen, Prakash Kulkarni, Ravi Salgia
Summary: In recent decades, the advancement of high-throughput approaches in cancer biology and medicine has led to the development of targeted therapies and immunotherapies for different cancers. The availability of diverse high-throughput omics data has revealed the complex nature of cancer as a system of microenvironments, sub-clonal tumor populations, and various cell types, impacting the genetic and non-genetic mechanisms involved in the disease. Taking a systems approach to cancer biology has been essential in understanding tumor initiation, progression, and drug resistance. Integrating clinical medicine with basic sciences has revolutionized the development and approval of cancer therapeutic drugs including tyrosine kinase inhibitors, antibody-drug conjugates, and immunotherapy. By further improving the 'Team Medicine' approach within the cancer systems biology framework, through the development of high-throughput clinical trial models utilizing machine learning and rapid sample processing, personalized medicine can advance more rapidly, overcoming limitations in drug development and testing.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Genetics & Heredity
Giuseppe Iacomino
Summary: miRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Dysregulation of miRNAs reflects the state and function of cells and tissues, contributing to their dysfunction. The identification of extracellular miRNAs in biological fluids highlights their potential as biomarkers, while their therapeutic potential is gaining attention. However, challenges such as stability, delivery systems, and bioavailability need to be addressed. Biopharmaceutical companies are increasingly involved in this field, and ongoing clinical trials suggest that anti-miR and miR-mimic molecules may have innovative therapeutic applications. This article provides an overview of pending issues and new opportunities offered by miRNAs in disease treatment and early diagnostics.
Editorial Material
Multidisciplinary Sciences
Nivedita Saxena, Michael Rendl
Summary: Combined imaging and gene-expression analyses have shown that the arrangement of cells in concentric rings in disc-like structures that form hair follicles can predetermine their fate and location in mature follicles.
Review
Biochemistry & Molecular Biology
Emily Samuela Turilli, Marta Lualdi, Mauro Fasano
Summary: The outbreak of the SARS-CoV-2 pandemic has driven the scientific community to seek rapid solutions to cope with the health emergency. The complexity of COVID-19 in terms of clinical outcomes, severity, and therapy response suggests the use of multifactorial strategies and systems biology approaches. Proteomics, interactomics, and artificial intelligence tools have been used to understand the pathobiology of COVID-19, identify drug targets, and repurpose drugs.
Review
Oncology
James H. Park, Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P. Patel, Santosh Kesari, Sui Huang, Nitin S. Baliga
Summary: Pronounced differences between individuals and cell-cell heterogeneity within tumors are major obstacles in effective brain tumor treatment, necessitating a personalized precision medicine approach. A systems biology approach is crucial for developing a multiscale understanding of disease mechanisms. Integrating patient tumor analysis with clinical medicine can optimize treatment strategies.
Article
Environmental Sciences
Gargi Chatterjee, Sangeeta Negi, Supratim Basu, Joel Faintuch, Anthonia O'Donovan, Pratyoosh Shukla
Summary: Microbial communities in the human intestine, known as microbiota, play a significant role in modulating human health, particularly in host immunity and neuronal signaling. Systemic analysis of the gut microbiome and microbiome engineering have been of great interest among scientists in understanding the complex interactions between the host and microbes and developing targeted precision medicine. Additionally, combining metabolic network analysis and multiple datasets can help identify specific metabolites. Potential therapeutic approaches like fecal microbiota transplant and integration of cellular models and computational models can shed light on the complex interactome of diet-microbiota-disease pathophysiology.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Chemistry, Multidisciplinary
Camila Guindani, Lucas Caire da Silva, Shoupeng Cao, Tsvetomir Ivanov, Katharina Landfester
Summary: Bottom-up synthetic biology is the scientific approach of building systems that imitate the structure and function of living cells from the ground up. Recent developments have allowed scientists to engineer synthetic cells and organelles that mimic the essential functions and behaviors of natural cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Gastroenterology & Hepatology
Claudio Fiocchi, Dimitrios Iliopoulos
Summary: Systems biology is a rapidly advancing field that offers new insights into disease mechanisms, patient diagnosis, and drug development. By integrating omics-derived big data to identify biological networks and develop specific blockers, systems biology has the potential to revolutionize therapeutic strategies for complex diseases like IBD. Although still in its early stages, the implementation of systems biology in IBD research holds great promise for advancing our understanding and improving patient outcomes.
INFLAMMATORY BOWEL DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Hui Jian, Yun Zhang, Junyue Wang, Zhenxiang Chen, Tingyi Wen
Summary: This study proposes a strategy to enhance the effect of chemodynamic therapy (CDT) by targeting abnormal glutamine metabolism in cancer cells. The researchers developed iron-doped zeolitic imidazolate frameworks (ZIF(Fe) NPs) to co-deliver a drug called telaglenastat (CB-839) and Fe2+ into the tumor. The inhibition of glutamine metabolism by CB-839 amplifies Fe2+-induced oxidative stress and reduces nucleotide pools, leading to enhanced cell-killing effect of CDT. In vivo assessments confirm the improved anticancer performance and biocompatibility of the developed nanoparticles.
Article
Health Care Sciences & Services
Seung Han Baek, Dinah Foer, Katherine N. Cahill, Elliot Israel, Enrico Maiorino, Annika Rohl, Joshua A. Boyce, Scott T. Weiss
Summary: The study found that strong responders to imatinib (FEV1 increase >20%) shared multiple downregulated mitochondrial-related pathways, while weak responders (5-10% FEV1 increase) and non-responders did not have these pathways in common.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Biotechnology & Applied Microbiology
Elizabeth Pavez Lorie, Sarah Baatout, Alexander Chouker, Judith-Irina Buchheim, Bjorn Baselet, Cinzia Dello Russo, Virginia Wotring, Monica Monici, Lucia Morbidelli, Dimitri Gagliardi, Julia Caroline Stingl, Leonardo Surdo, Vincent Lai Ming Yip
Summary: Personalized medicine aims to improve patient health by individualizing disease prevention, diagnosis, and treatment based on variations in response to environmental factors and treatments. Space travel exposes individuals to environmental stressors leading to physiological adaptations, showing significant inter-individual variability in health responses.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Anna L. Kersey, Thuy-Uyen Nguyen, Biswadeep Nayak, Irtisha Singh, Akhilesh K. Gaharwar
Summary: Recent developments in biomedical engineering have focused on designing smart and bio-responsive materials. Recent technological advances in biology, specifically in omics techniques, can provide high-throughput functional readouts of the cellular and molecular interactions. These omics-based approaches have the potential to revolutionize biomedical research and replace traditional trial and error approaches in designing the next-generation of biomaterials.
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Cell Biology
Harald Hampel, Robert Nistico, Nicholas T. Seyfried, Allan I. Levey, Erica Modeste, Pablo Lemercier, Filippo Baldacci, Nicola Toschi, Francesco Garaci, George Perry, Enzo Emanuele, Pedro L. Valenzuela, Alejandro Lucia, Andrea Urbani, Giulia M. Sancesario, Mark Mapstone, Massimo Corbo, Andrea Vergallo, Simone Lista
Summary: Alzheimer's disease is characterized by complex pathophysiology with high heterogeneity, requiring a holistic approach to fully capture its multifaceted nature. Integrating omics sciences and systems biology network approaches can help detect and describe the biological changes occurring in the progression of AD.
AGEING RESEARCH REVIEWS
(2021)
Article
Neurosciences
Brianna Gurdon, Catherine Kaczorowski
Summary: Alzheimer's disease is a complex disease mediated by numerous factors, with research focusing on how imaging modalities can be integrated into systems biology approaches to understand the genotype to phenotype relationship driving disease development. By combining imaging and omics data, AD can be classified into subtypes, paving the way for precision medicine solutions to prevent and treat the disease.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Cell Biology
Praveen Vasudevan, Ralf Gaebel, Piet Doering, Paula Mueller, Heiko Lemcke, Jan Stenzel, Tobias Lindner, Jens Kurth, Gustav Steinhoff, Brigitte Vollmar, Bernd Joachim Krause, Hueseyin Ince, Robert David, Cajetan Immanuel Lang
Article
Cell Biology
Sarah Sasse, Anna Skorska, Cornelia Aquilina Lux, Gustav Steinhoff, Robert David, Ralf Gaebel
Article
Cell Biology
Cajetan Immanuel Lang, Piet Doering, Ralf Gaebel, Praveen Vasudevan, Heiko Lemcke, Paula Mueller, Jan Stenzel, Tobias Lindner, Markus Joksch, Jens Kurth, Carina Bergner, Hans-Juergen Wester, Hueseyin Ince, Gustav Steinhoff, Brigitte Vollmar, Robert David, Bernd Joachim Krause
Article
Medicine, General & Internal
Markus Wolfien, Denise Klatt, Amankeldi A. Salybekov, Masaaki Ii, Miki Komatsu-Horii, Ralf Gaebel, Julia Philippou-Massier, Eric Schrinner, Hiroshi Akimaru, Erika Akimaru, Robert David, Jens Garbade, Jan Gummert, Axel Haverich, Holger Hennig, Hiroto Iwasaki, Alexander Kaminski, Atsuhiko Kawamoto, Christian Klopsch, Johannes T. Kowallick, Stefan Krebs, Julia Nesteruk, Hermann Reichenspurner, Christian Ritter, Christof Stamm, Ayumi Tani-Yokoyama, Helmut Blum, Olaf Wolkenhauer, Axel Schambach, Takayuki Asahara, Gustav Steinhoff
Article
Cell Biology
Praveen Vasudevan, Markus Wolfien, Heiko Lemcke, Cajetan Immanuel Lang, Anna Skorska, Ralf Gaebel, Dirk Koczan, Tobias Lindner, Robby Engelmann, Brigitte Vollmar, Bernd Joachim Krause, Olaf Wolkenhauer, Hermann Lang, Gustav Steinhoff, Robert David
Article
Biochemistry & Molecular Biology
Nicole Zarniko, Anna Skorska, Gustav Steinhoff, Robert David, Ralf Gaebel
Editorial Material
Cell Biology
Gustav Steinhoff
Review
Oncology
M. Hornschuh, E. Wirthgen, M. Wolfien, K. P. Singh, O. Wolkenhauer, J. Daebritz
Summary: Epigenetics plays a crucial role in inflammatory bowel diseases, particularly in Crohn's disease, which is believed to be a result of a complex interplay between genetic susceptibility, environmental factors, and altered intestinal microbiota. While many genetic variants have been associated with Crohn's disease, the influence of epigenetics in its pathogenesis remains relatively unknown.
CLINICAL EPIGENETICS
(2021)
Article
Multidisciplinary Sciences
Cajetan Immanuel Lang, Praveen Vasudevan, Piet Doering, Ralf Gaebel, Heiko Lemcke, Tobias Lindner, Gustav Steinhoff, Bernd Joachim Krause, Brigitte Vollmar, Felix G. Meinel, Seyrani Yuecel, Alper Oener, Hueseyin Ince, Robert David
Summary: This study investigated post-infarct remodeling after acute myocardial infarction using mouse models and magnetic resonance imaging. The results showed differences in cardiac remodeling between the permanent ligation (PL) and ischemia reperfusion (I/R) models. Different methods of analysis revealed that PL resulted in significant left ventricle dilation and decreased contractile function, while the effects were less pronounced in the I/R model.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Saptarshi Bej, Anne-Marie Galow, Robert David, Markus Wolfien, Olaf Wolkenhauer
Summary: The study presents a machine learning-based oversampling method for identifying rare-cell subpopulations in single-cell and single-nuclei RNA-sequencing data. By generating synthetic cells, the approach effectively identifies similar rare cells in other publicly available experiments, demonstrating a robust precision-recall balance for rare-cell detection.
BMC BIOINFORMATICS
(2021)
Review
Cell Biology
Amankeldi A. Salybekov, Markus Wolfien, Shuzo Kobayashi, Gustav Steinhoff, Takayuki Asahara
Summary: Stem/progenitor cell transplantation is a potential therapy for inducing angiogenesis in ischemic tissue and preventing major amputation in patients with advanced PAD. However, clinical studies have shown varying responses among patients, suggesting the influence of unidentified risk factors. Personalized stem cell-based therapy by analyzing individual risk factors may improve treatment efficacy, but integrating complex approaches for patient identification before therapy remains a significant challenge.
Article
Biochemistry & Molecular Biology
Beschan Ahmad, Anna Skorska, Markus Wolfien, Haval Sadraddin, Heiko Lemcke, Praveen Vasudevan, Olaf Wolkenhauer, Gustav Steinhoff, Robert David, Ralf Gaebel
Summary: This study investigated the effects of mesenchymal stem cell (MSC) injection on post-infarction arrhythmias. The results showed that MSC therapy after double infarction significantly reduced simple and complex arrhythmias. RNA sequencing analysis also revealed a decline in arrhythmias and reduced inflammatory pathways. Additionally, the study identified highly expressed genes linked to lowering the risk of heart failure, cardiomyopathy, and sudden cardiac death.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Clinical Neurology
Stephan C. Knipp, Torulv Holst, Konstantinos Bilbilis, Otgonzul von Velsen, Claudia Ose, Hans-Christoph Diener, Heinz Jakob, Arjang Ruhparwar, Karl-Heinz Joeckel, Christian Weimar
Summary: In patients with coronary artery disease and asymptomatic severe carotid stenosis, the risk of stroke or death is higher following combined CABG+CEA compared with CABG alone. However, there is no significant difference in long-term outcomes after 5 years.
Article
Computer Science, Artificial Intelligence
Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
Summary: This article introduces a method, LoRAS, that overcomes the limitations of SMOTE oversampling technique, and through experiments, proves that LoRAS generates better machine learning models on imbalanced datasets, improving F1-Score and balanced accuracy. Compared to most SMOTE extensions, LoRAS achieves better results in generating classification models.
Review
Biochemistry & Molecular Biology
Yanli Liu, Rongcheng Niu, Wenzhong Li, Juntang Lin, Christof Stamm, Gustav Steinhoff, Nan Ma
CELLULAR AND MOLECULAR LIFE SCIENCES
(2019)