Systems biology: current status and challenges

Županič, Anže; Bernstein, Hans C.; Heiland, Ines

doi:10.1007/s00018-019-03410-z

Cited by 22 publications

(14 citation statements)

References 9 publications

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“…Systems biology is an area of research that aims to understand the mechanisms of complex biological systems and predict their behavior across scales: molecular-to-organismal (13). This approach allows us to embrace the complexity of a system and the, often degenerate, interactions between its components as a fundamental feature of the network.…”

Section: Systems Biologymentioning

confidence: 99%

Progress in kidney transplantation: The role for systems immunology

et al. 2022

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The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.

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Section: Systems Biologymentioning

confidence: 99%

Progress in kidney transplantation: The role for systems immunology

et al. 2022

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“…Due to the availability and storage of the extensive amount of molecular data, an urgent demand has developed as a new branch of science: “system biology,” which unravels the basic functional properties of living beings originating from the interaction of macromolecules ( Zupanic et al, 2020 ). The increased ability to elucidate genetic variations and their role in downstream molecular changes, like metabolite levels, would play a crucial role in interpreting and combining various data types.…”

Section: Identification Of Therapeutic Biomolecules Of Plants Through the Multi-omics Approachmentioning

confidence: 99%

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

Singh

Kumar

et al. 2021

Front. Pharmacol.

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COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.

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“…The rapid development of systemic biology provides a powerful tool for exploring disease-associated genes ( 6 ). Weighted gene co-expression network analysis (WGCNA) is a novel systemic biology analysis approach ( 7 ) that divides the gene expression matrix into different gene modules and detects the relationship between gene modules and external phenotypical characteristics.…”

Section: Introductionmentioning

confidence: 99%

Weighted gene co-expression network analysis identifies dysregulated B-cell receptor signaling pathway and novel genes in pulmonary arterial hypertension

Chen

Wang

et al. 2022

Front. Cardiovasc. Med.

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BackgroundPulmonary arterial hypertension (PAH) is a devastating cardio-pulmonary vascular disease in which chronic elevated pulmonary arterial pressure and pulmonary vascular remodeling lead to right ventricular failure and premature death. However, the exact molecular mechanism causing PAH remains unclear.MethodsRNA sequencing was used to analyze the transcriptional profiling of controls and rats treated with monocrotaline (MCT) for 1, 2, 3, and 4 weeks. Weighted gene co-expression network analysis (WGCNA) was employed to identify the key modules associated with the severity of PAH. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential biological processes and pathways of key modules. Real-time PCR and western blot analysis were used to validate the gene expression. The hub genes were validated by an independent dataset obtained from the Gene Expression Omnibus database.ResultsA total of 26 gene modules were identified by WGCNA. Of these modules, two modules showed the highest correlation with the severity of PAH and were recognized as the key modules. GO analysis of key modules showed the dysregulated inflammation and immunity, particularly B-cell-mediated humoral immunity in MCT-induced PAH. KEGG pathway analysis showed the significant enrichment of the B-cell receptor signaling pathway in the key modules. Pathview analysis revealed the dysregulation of the B-cell receptor signaling pathway in detail. Moreover, a series of humoral immune response-associated genes, such as BTK, BAFFR, and TNFSF4, were found to be differentially expressed in PAH. Additionally, five genes, including BANK1, FOXF1, TLE1, CLEC4A1, and CLEC4A3, were identified and validated as the hub genes.ConclusionThis study identified the dysregulated B-cell receptor signaling pathway, as well as novel genes associated with humoral immune response in MCT-induced PAH, thereby providing a novel insight into the molecular mechanisms underlying inflammation and immunity and therapeutic targets for PAH.

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Systems biology: current status and challenges

Cited by 22 publications

References 9 publications

Progress in kidney transplantation: The role for systems immunology

Progress in kidney transplantation: The role for systems immunology

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

Weighted gene co-expression network analysis identifies dysregulated B-cell receptor signaling pathway and novel genes in pulmonary arterial hypertension

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