Review
Biochemistry & Molecular Biology
Anna Campanati, Andrea Marani, Emanuela Martina, Federico Diotallevi, Giulia Radi, Annamaria Offidani
Summary: Psoriasis is an immune-mediated inflammatory disease that affects 2-3% of the worldwide population, with biologics being able to modify the natural history of the disease by reducing inflammation and preventing organ damage and systemic complications.
Article
Allergy
Cristina Segu-Verges, Jessica Gomez, Pau Terradas-Montana, Laura Artigas, Serge Smeets, Marta Ferrer, Sinisa Savic
Summary: Chronic spontaneous urticaria (CSU) is a rare and severely debilitating skin disease. This study used systems biology and machine learning to create a CSU interactome model and identified the mechanism of action of different therapeutic strategies.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Review
Immunology
Vinee Purohit, Allon Wagner, Nir Yosef, Vijay K. Kuchroo
Summary: Technical advances at the interface of biology and computation, such as single-cell RNA-sequencing (scRNA-seq), have uncovered new levels of complexity in cellular systems. The study of immune cell metabolism has emerged as a new area of investigation using the systems biology approach. However, there are several challenges, including the diversity of immune cell phenotypes, sparse immune cell numbers in vivo, limitations in metabolite identification, dynamic nature of cellular metabolism and metabolic fluxes, tissue specificity, and dependence on the local milieu. This review discusses the systemic nature of immunometabolism, cell- and system-based approaches, mathematical modeling techniques, and applications and challenges in metabolic modeling.
CELLULAR & MOLECULAR IMMUNOLOGY
(2022)
Review
Immunology
Denis A. Mogilenko, Alexey Sergushichev, Maxim N. Artyomov
Summary: Immunometabolism has become a new interdisciplinary field of research in recent years, providing important insights into the regulation of immune responses. Traditional approaches and new technologies, such as spatially resolved metabolic imaging and computational algorithms, have helped us understand the complexity of immunometabolic regulation. This review discusses recent studies and technological developments that aim to capture the interplay between immune responses and metabolism.
ANNUAL REVIEW OF IMMUNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Junjie Peng, Elizabeth C. Jury, Pierre Donnes, Coziana Ciurtin
Summary: Machine learning applications in the clinical study of chronic inflammatory diseases show promising results and potential for precision medicine, aiding in prediction, diagnosis, prognosis, disease management, and drug development.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Immunology
Douglas Fritz, Jun Inamo, Fan Zhang
Summary: Recent advances in single-cell sequencing technologies have revealed the heterogeneity of fibroblasts and their potential clinical significance in inflammatory diseases. Computational techniques, including machine learning, have played a crucial role in categorizing fibroblast subpopulations and their interactions with other immune cells. These computational omics approaches have the potential to contribute to therapeutic strategies for inflammatory diseases by targeting fibroblast-macrophage interactions.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andres Tittarelli
Summary: Connexin-mediated intercellular communication mechanisms play important roles in immune system activities, especially in infections, wounds, cancer, and other inflammatory conditions. Modulating connexin expression and channel activities may be a promising approach for designing therapeutic tools.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Review
Gastroenterology & Hepatology
Joan Claria, Vicente Arroyo, Richard Moreau
Summary: Acute-on-chronic liver failure (ACLF) is the most severe form of acutely decompensated cirrhosis and is characterized by intense systemic inflammation and various mechanisms that lead to organ failures, including vasodilation, neutrophil migration, microthrombi formation, hepatic encephalopathy, and energy competition.
Article
Cardiac & Cardiovascular Systems
Jan M. Griffin, Hannah Rosenblum, Mathew S. Maurer
Summary: Cardiac amyloidosis, once considered a rare disease, is now increasingly recognized due to aging population and noninvasive diagnostic methods. Better understanding of the pathogenesis of cardiac amyloidosis has led to the development of multiple effective therapies.
CIRCULATION RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Angela Saez, Beatriz Herrero-Fernandez, Raquel Gomez-Bris, Hector Sanchez-Martinez, Jose M. M. Gonzalez-Granado
Summary: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is a chronic intestinal inflammation with an unknown cause. Innate immune cells (IICs), such as neutrophils, monocytes, macrophages, and dendritic cells, play a crucial role in defending against pathogens and maintaining immune tolerance. An imbalance in the innate immune response is closely linked to intestinal inflammation and IBD. Understanding the mechanisms and interactions of IICs with other immune cells is essential for developing effective therapies for IBD patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pharmacology & Pharmacy
Sarah Smith, Raimondo Ascione
Summary: Myocardial healing following myocardial infarction depends on the complex interplay between nervous and immune system responses, ischemia/reperfusion injury factors, as well as genetic and epidemiological factors. Targeting the neuro-immune systems may induce beneficial effects on cardiac tissue repair post MI, indicating an overarching synergic response across these systems.
PHARMACOLOGY & THERAPEUTICS
(2023)
Review
Immunology
Alexis Hoerter, Eusondia Arnett, Larry S. Schlesinger, Elsje Pienaar
Summary: Coinfection with HIV and tuberculosis increases the risk of active tuberculosis and is the leading cause of death in HIV positive individuals. Tuberculosis granulomas, the sites of host-pathogen interactions, play a crucial role in understanding and treating coinfection. Coupling computational modeling with in vitro and in vivo experiments can accelerate discoveries in Mtb-HIV coinfection.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Marina Amaral Alves, Santosh Lamichhane, Alex Dickens, Aidan McGlinchey, Henrique Caracho Ribeiro, Partho Sen, Fang Wei, Tuulia Hyotylainen, Matej Oresic
Summary: Lipids play important roles in biology, such as energy storage and cell membrane structure. Lipid metabolism is tightly regulated, and disturbances in lipid-related pathways are involved in the pathogenesis of common diseases. Advances in lipidomics provide new methods for lipid research.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2021)
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)
Article
Biochemical Research Methods
Shan-Ju Yeh, Bor-Sen Chen
Summary: This study proposes a systematic approach to investigate the molecular progression mechanisms of gastric cancer and identifies critical biomarkers and corresponding drugs. By utilizing big database mining, system modeling, and deep learning techniques, the study successfully reveals the progression of gastric cancer and suggests potential multi-target drugs.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)