Article
Immunology
Julia Nakanishi Usuda, Desiree Rodrigues Placa, Dennyson Leandro M. Fonseca, Alexandre H. C. Marques, Igor Salerno Filgueiras, Victor Gabriel Bastos Chaves, Anny Silva Adri, Amanda Torrentes-Carvalho, Mario Hiroyuki Hirata, Paula Paccielli Freire, Rusan Catar, Gustavo Cabral-Miranda, Lena F. Schimke, Guido Moll, Otavio Cabral-Marques
Summary: This study characterizes the landscape of the interferome signature in DENV infection, highlighting the crucial role of interferome dynamics in the anti-dengue immune response, and identifies potential biomarkers for disease severity.
FRONTIERS IN 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
Endocrinology & Metabolism
Taylor Landry, Daniel Shookster, Hu Huang
Summary: ROCK1 plays important roles in metabolism, with potential as a therapeutic target in diabetes and obesity. Recent advances in tissue-specific approaches have helped to uncover its critical metabolic functions.
FRONTIERS IN ENDOCRINOLOGY
(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
Oncology
Lorella Tripodi, Emanuele Sasso, Sara Feola, Ludovica Coluccino, Maria Vitale, Guido Leoni, Barbara Szomolay, Lucio Pastore, Vincenzo Cerullo
Summary: This review provides a roadmap for the development of safe and effective future therapeutics based on oncolytic viruses (OVs) using synthetic and systems biology strategies. Integration of system and synthetic biology can improve the design of OVs by retaining virulence-associated genes and refining target discovery in different types of cancer. By using specific computation pipelines, it is possible to identify MHC-I and II-restricted peptide repertoire recognized by T-cells and enhance anticancer immune responses. These approaches can overcome challenges and improve the efficacy and safety profile of OVs-based therapies.
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
Biochemistry & Molecular Biology
Anupama Khare
Summary: Recent studies utilizing experimental systems biology techniques to explore interactions in simplified model microbial communities have identified novel interactions and described underlying genetic and molecular mechanisms. Integration of these and targeted methods provides comprehensive insights into species interactions in microbial communities.
TRENDS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Tim Diederichs, Robert Tampe
Summary: Cellular life relies on transport and communication across membranes, making membrane proteins prime drug targets. Researchers have successfully reconstituted membrane assemblies using giant liposomes, demonstrating the unidirectional transport of substrates by nanomachineries. This approach enables the construction of delicate artificial cell-like systems for real-time tracking of substrate transport.
Review
Immunology
Khushboo Borah, Ye Xu, Johnjoe McFadden
Summary: Tuberculosis is a devastating infectious disease that kills over a million people annually, with increasing challenges of multi and extensively drug resistant strains. Host-pathogen interactions, metabolic cross talk, and advancements in systems-based omic technologies play critical roles in TB research and offer promising interventions for anti-TB therapies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nathan L. Mellor, Ute Voss, Alexander Ware, George Janes, Duncan Barrack, Anthony Bishopp, Malcolm J. Bennett, Markus Geisler, Darren M. Wells, Leah R. Band
Summary: Members of the B family of membrane-bound ATP-binding cassette (ABC) transporters play important roles in auxin efflux in plants. This study integrates ABCB localization data into a multicellular model to predict the impact of ABCB-mediated auxin transport on organ-scale distribution. The results suggest that ABCBs enable auxin efflux independently of PINs, but PINs predominantly mediate auxin efflux when co-localized with ABCBs.
Article
Immunology
Yan Wang, Hongxia Jia, Wei Li, Hongping Liu, Meng Tu, Jing Li, Jiuling Cheng, Guojun Zhang
Summary: This study investigated the correlation between anti-MDA5 antibody titers and type I IFN signature in patients with MDA5+ DM. Transcriptome profiling of PBMCs in MDA5+ DM patients revealed enrichment of differentially expressed genes related to viral and cytokine pathways. Significant correlations were found between anti-MDA5 titers and type I IFN scores, and higher titers were observed in patients with ultra-high type I IFN scores. Furthermore, the asynchrony between type I IFN scores and anti-MDA5 titers was observed during the course of treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Genetics & Heredity
Taylor M. Weiskittel, Cristina Correia, Grace T. Yu, Choong Yong Ung, Scott H. Kaufmann, Daniel D. Billadeau, Hu Li
Summary: Machine learning plays a crucial role in bridging the analytical gaps in single-cell studies and works synergistically with single-cell data. System biology algorithms have integrated machine learning with biological components to provide system-level analyses of single-cell omics data, shedding light on complex biological mechanisms.
Article
Biodiversity Conservation
Hannah J. Calich, Jorge P. Rodriguez, Victor M. Eguiluz, Neil Hammerschlag, Charitha Pattiaratchi, Carlos M. Duarte, Ana M. M. Sequeira
Summary: This study analyzed satellite tracking data from three co-occurring apex predators to identify high interspecific variability in shark movement patterns and search strategies. Tiger sharks displayed near-random movements, great hammerheads showed a mixed-movement strategy, and bull sharks followed a resident movement strategy. The species-specific search strategies identified here may help foster the co-existence of these sympatric apex predators.
Article
Virology
Mohammad-Moien Forghani-Ramandi, Behnam Mostafavi, Atefeh Bahavar, Maryam Dehghankar, Zeinab Siami, Sayed-Hamidreza Mozhgani
Summary: This study used bioinformatics methods to investigate the expression of genes and the affected cellular signaling pathways in adult T-cell leukemia/lymphoma (ATLL). The results revealed the key roles of pathways related to immune response regulation, T-cell receptor and activation, regulation of cell signaling, Wnt signaling pathway, and apoptosis in the pathogenesis of ATLL. Possible biomarkers were also identified. Further research is needed to validate these genes as biomarkers and treatment targets.
Article
Biochemical Research Methods
Jong Hyun Park, Marcelo C. Bassalo, Geng-Min Lin, Ye Chen, Hamid Doosthosseini, Joep Schmitz, Johannes A. Roubos, Christopher A. Voigt
Summary: The optimization of cellular functions often requires balancing gene expression, which is costly and time-consuming. In this study, a strain of Saccharomyces cerevisiae was constructed with a sensor array containing bacterial regulators that respond to small molecule inducers. This approach allows for the study of gene expression without the need for multiple strain constructions and was applied to optimize a four-gene heterologous pathway. This work has the potential to aid in the rapid automated development of yeasts for bio-manufacturing diverse products.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Darawan Rinchai, Jessica Roelands, Mohammed Toufiq, Wouter Hendrickx, Matthew C. Altman, Davide Bedognetti, Damien Chaussabel
Summary: This study introduces an R package, BloodGen3Module, to facilitate group comparison analyses at the module level and display results as annotated fingerprint grid plots. Additionally, it provides a parallel workflow for computing module repertoire changes for individual samples and displays results as fingerprint heatmaps. This resource aims to assist in analyzing and interpreting changes in blood transcript abundance across various pathological and physiological states.
Article
Microbiology
Mikiko Izaki, Jun-ichirou Yasunaga, Kisato Nosaka, Kenji Sugata, Hayato Utsunomiya, Youko Suehiro, Takafumi Shichijo, Asami Yamada, Yasuhiko Sugawara, Taizo Hibi, Yukihiro Inomata, Hirofumi Akari, Anat Melamed, Charles Bangham, Masao Matsuoka
Summary: HTLV-1 spreads in vivo through two routes: de novo infection and clonal proliferation of infected cells. Host immune responses play a critical role in maintaining and increasing PVL. Infected clones tend to survive long-term in vivo, with the immune properties of these clones playing an important role in clonal proliferation.
Article
Immunology
Hiroo Katsuya, Lucy B. M. Cook, Aileen G. Rowan, Anat Melamed, Jocelyn Turpin, Jumpei Ito, Saiful Islam, Paola Miyazato, Benjy Jek Yang Tan, Misaki Matsuo, Toshikazu Miyakawa, Hirotomo Nakata, Shuzo Matsushita, Graham P. Taylor, Charles R. M. Bangham, Shinya Kimura, Yorifumi Satou
Summary: Coinfection with HIV-1 and HTLV-1 alters the distribution of viral integration sites and clonality of virus-infected cells, potentially impacting the risks associated with both HTLV-1 and HIV-1-related diseases.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Editorial Material
Hematology
Charles R. M. Bangham
Summary: In this study, Kogure et al identify new oncogenic drivers, noncoding and structural mutations, and a novel molecular signature that distinguishes the leukemic from the lymphomatous forms of adult T-cell leukemia/lymphoma (ATL) through a whole-genome analysis of 150 cases.
Correction
Immunology
Hiroo Katsuya, Lucy B. M. Cook, Aileen G. Rowan, Anat Melamed, Jocelyn Turpin, Jumpei Ito, Saiful Islam, Paola Miyazato, Benjy Jek Yang Tan, Misaki Matsuo, Toshikazu Miyakawa, Hirotomo Nakata, Shuzo Matsushita, Graham P. Taylor, Charles R. M. Bangham, Shinya Kimura, Yorifumi Satou
JOURNAL OF INFECTIOUS DISEASES
(2022)
Review
Cardiac & Cardiovascular Systems
Sarah Halawa, Soni S. Pullamsetti, Charles R. M. Bangham, Kurt R. Stenmark, Peter Dorfmuller, Maria G. Frid, Ghazwan Butrous, Nick W. Morrell, Vinicio A. de Jesus Perez, David I. Stuart, Kevin O'Gallagher, Ajay M. Shah, Yasmine Aguib, Magdi H. Yacoub
Summary: This article discusses the potential causes of COVID-19 heterogeneity and summarizes the pathobiology of the disease, with a focus on the role of the pulmonary vasculature in the acute stage and the potential for developing chronic pulmonary hypertension.
NATURE REVIEWS CARDIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexander J. Mentzer, Nicole Brenner, Naomi Allen, Thomas J. Littlejohns, Amanda Y. Chong, Adrian Cortes, Rachael Almond, Michael Hill, Simon Sheard, Gil McVean, Rory Collins, Adrian V. S. Hill, Tim Waterboer
Summary: The authors designed a multiplex serology platform to measure quantitative antibody responses against 20 infectious agents and confirmed their associations with sociodemographic characteristics, HLA genetic variants, and disease outcomes. The findings provide valuable insights into host-pathogen-disease relationships.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Anat Melamed, Tomas W. Fitzgerald, Yuchuan Wang, Jian Ma, Ewan Birney, Charles R. M. Bangham
Summary: Human retroviruses HTLV-1 and HIV-1 persist in the body as a reservoir of latently infected T cell clones. The study found that the position of the provirus in the nucleus, its distance from the centromere, and the intensity of local host genome transcription are important factors determining clonal survival. Similar factors were also found to explain clonal persistence of HIV-1. This research highlights the importance of the intranuclear and intrachromosomal location of the provirus and host transcription intensity in the persistence of human retroviruses.
Article
Immunology
Annika P. Schnell, Stephan Kohrt, Aris Aristodemou, Graham P. Taylor, Charles R. M. Bangham, Andrea K. Thoma-Kress
Summary: The pan-HDACi Panobinostat and class I HDACi Romidepsin have been identified as potent agents in enhancing Tax expression in HTLV-1. However, the increase in Tax protein levels is only moderate.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Christy Prawiro, Tom D. Bunney, Charis Kampyli, Hiroko Yaguchi, Matilda Katan, Charles R. M. Bangham
Summary: Adult T-cell leukemia/lymphoma (ATL) development involves HTLV-1 infection and somatic mutations, with phospholipase C gamma1 (PLCG1) being the most frequently mutated gene. The functional consequences of PLCG1 mutations in cancer cells have not been characterized.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Microbiology
Saumya Ramanayake, Dale A. Moulding, Yuetsu Tanaka, Abhyudai Singh, Charles R. M. Bangham
Summary: We studied the kinetics of Tax expression in two naturally-infected, non-malignant T-cell clones using live-cell imaging and mathematical modeling. Single-cell analysis revealed five patterns of Tax expression, with most Tax-positive cells expressing continuously over a 30-hour period. The average duration of Tax expression in the two clones was 94 and 417 hours, respectively, as estimated by mathematical modeling. Tax expression was associated with transiently decreased proliferation, increased apoptosis, enhanced activation of DNA damage response pathways, and delayed progression through the cell cycle. Extended observation showed that as cells ceased Tax expression, there was an increase in the proportion of proliferating cells and a decrease in the percentage of apoptotic cells, resulting in a greater net growth of the initially Tax-positive population. Tax-expressing cells also formed cell clumps and exhibited reduced cell movement. These findings help reconcile previous conflicting observations regarding the impact of Tax on the host cell.
Review
Hematology
Charles R. M. Bangham
Summary: Human T-cell leukemia virus type 1 (HTLV-1) causes ATL in 5% of infected people and HTLV-1-associated myelopathy in 0.3% to 4% of them. Reliable treatments are lacking, but there have been recent advances in ATL prevention and treatment. Understanding the virus's persistence in the host and its role in oncogenesis is crucial.
Article
Microbiology
Aris E. N. R. Aristodemou, David Rueda, Graham R. Taylor, Charles R. M. Bangham, Patrick L. R. Green
Summary: This study analyzed the expression changes of host and viral genes during HTLV-1 reactivation in cells isolated from patients' blood. The study found that changes in viral expression may be related to changes in a group of epigenetic modifiers, which may contribute to the virus returning to a latent state after activation. In addition, the study also identified three deubiquitinases that can promote viral expression. These findings are of great importance for further understanding the lifecycle and infection mechanisms of HTLV-1.
Article
Immunology
Robert S. Wallis, Anne O'Garra, Alan Sher, Andreas Wack
Summary: This Perspective reflects on the historical development of host-directed immunotherapeutic interventions for viral and bacterial infections, and discusses their application to current approaches to therapy of SARS-CoV-2 and Mycobacterium tuberculosis infections.
NATURE REVIEWS IMMUNOLOGY
(2023)
Review
Clinical Neurology
Abelardo Araujo, Charles R. M. Bangham, Jorge Casseb, Eduardo Gotuzzo, Steve Jacobson, Fabiola Martin, Augusto Penalva de Oliveira, Marzia Puccioni-Sohler, Graham P. Taylor, Yoshihisa Yamano
Summary: Recent review of clinical studies on disease-modifying therapy for HAM/TSP concluded that high-dose pulsed methyl prednisolone is effective for induction, while low-dose oral prednisolone is recommended for maintenance therapy. However, there is not enough evidence to support the use of antiretroviral therapy or interferon-alpha as a first-line treatment for the disease.
NEUROLOGY-CLINICAL PRACTICE
(2021)