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RNA-Binding Proteins as Novel Effectors in Osteoblasts and Osteoclasts: A Systems Biology Approach to Dissect the Transcriptional Landscape.

Bone health is ensured by the coordinated action of two types of cells-the osteoblasts that build up bone structure and the osteoclasts that resorb the bone. The loss of balance in their action results in pathological conditions such as osteoporosis. Central to this study is a class of RNA-binding proteins (RBPs) that regulates the biogenesis of miRNAs. In turn, miRNAs represent a critical level of regulation of gene expression and thus control multiple cellular and biological processes. The impact of miRNAs on the pathobiology of various multifactorial diseases, including osteoporosis, has be

Bioinformatic and systems biology approach revealing the shared genes and molecular mechanisms between COVID-19 and non-alcoholic hepatitis.

Introduction: Coronavirus disease 2019 (COVID-19) has become a global pandemic and poses a serious threat to human health. Many studies have shown that pre-existing nonalcoholic steatohepatitis (NASH) can worsen the clinical symptoms in patients suffering from COVID-19. However, the potential molecular mechanisms between NASH and COVID-19 remain unclear. To this end, key molecules and pathways between COVID-19 and NASH were herein explored by bioinformatic analysis. Methods: The common differentially expressed genes (DEGs) between NASH and COVID-19 were obtained by differential gene analysis.

Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study.

Vitiligo is the most common cause of skin, hair, and oral depigmentation which is known as an autoimmune disorder. Genetic and environmental factors have important roles in the progression of the disease. Dysregulation of gene expression, like microRNAs (miRNA), may serve as major relevant factors. Several biological processes are involved in vitiligo disease and developing a comprehensive approach helps us to better understand the molecular mechanisms of disease. In this research, we describe how a weighted gene co-expression network analysis as a systems biology approach assists to define th…

A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host.

BACKGROUND: Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network. METHODS: In this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interacti

A systems biology approach to predictive developmental neurotoxicity of a larvicide used in the prevention of Zika virus transmission.

The need to prevent developmental brain disorders has led to an increased interest in efficient neurotoxicity testing. When an epidemic of m … itro or in silico, must be considered. We have developed a network-based model using an integrative systems biology approach to explore the potential developmental neurotoxicity, and we applied this method to examine the larvicide pyriproxyfen widely used in the prevention of Zika virus transmission. Our computational model covered a wide range of possible pathwa …

A systems BIOlogy Study to TAilored Treatment in Chronic Heart Failure: rationale, design, and baseline characteristics of BIOSTAT-CHF.

AIMS: Despite major improvements in pharmacological and device treatments, heart failure remains a syndrome with high morbidity and mortalit … -up phase, uptitration to guideline-recommended doses was encouraged. CONCLUSION: By using a novel systems biology approach, incorporating demographics, biomarkers, genome-wide analysis, and proteomics, a model that predicts response to therapy will be developed, which should be instrumental in developing alternative therapies for patients with suboptimal respon …

Systems Biology Approaches for the Prediction of Possible Role of Chlamydia pneumoniae Proteins in the Etiology of Lung Cancer.

Accumulating evidence has recently supported the association of bacterial infection with the growth and development of cancers, particularly in organs that are constantly exposed to bacteria such as the lungs, colon, cervical cancer etc. Our in silico study on the proteome of Chlamydia pneumoniae suggests an unprecedented idea of the etiology of lung cancer and have revealed that the infection of C. pneumoniae is associated with lung cancer development and growth. It is reasonable to assume that C. pneumoniae transports its proteins within host-intracellular organelles during infection, where

New insights into the pathogenesis of tuberculosis revealed by Mycobacterium marinum: the zebrafish model from the systems biology perspective.

Tuberculosis remains a worldwide health concern, largely due to the emergence of multi-drug-resistant (MDR) and extensive-drug-resistant (XD … l, zebrafish provide unprecedented opportunities to address the pathogenesis of tuberculosis from a systems biology perspective. The latest data from this model are summarized in this review, special attention is given to the shared pathway and network between zebrafish and humans. This research serves to deepen our understanding of this complex process and to pr …

Ulnar ray deficiency: a review of the classification systems, the clinical features in 72 cases, and related developmental biology.

Ulnar ray deficiency is rare and has a variable presentation. As a result, there are many different classification systems for this anomaly. Furthermore, the developmental biology of the anomaly is still not fully understood. The aim of this article is to review the previous classification systems, present the clinical features in 72 cases and discuss the developmental biology of ulnar ray deficiency.

Systems biology of autosomal dominant polycystic kidney disease (ADPKD): computational identification of gene expression pathways and integrated regulatory networks.

To elucidate the molecular pathways that modulate renal cyst growth in ADPKD, we performed global gene profiling on cysts of different size (<1 ml, n = 5; 10-20 ml, n = 5; >50 ml, n = 3) and minimally cystic tissue (MCT, n = 5) from five PKD1 human polycystic kidneys using Affymetrix HG-U133 Plus 2.0 arrays. We used gene set enrichment analysis to identify overrepresented signaling pathways and key transcription factors (TFs) between cysts and MCT. We found down-regulation of kidney epithelial restricted genes (e.g. nephron segment-specific markers and cilia-associated cystic genes such as HNF

A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells.

Genome-scale metabolic models (GEMs) are indispensable for studying cellular metabolism. We present iCHO3K, a community-consensus, manually curated reconstruction of the Chinese hamster metabolic network. Spanning 11,004 reactions linked to 3,597 genes, iCHO3K augments the network with 3,489 protein structures and physicochemical descriptors for >70% of 7,377 metabolites, enabling structure-aware analyses. We applied iCHO3K to contextualize transcriptomics and metabolomics from a fed-batch Chinese hamster ovary (CHO) cell line engineered to abolish lactate secretion. The model indicated reduce

Multi-omics analysis reveals mechanisms of Qingying granules in treating porcine warm disease: dosage optimization and systems biology insights.

BACKGROUND: Warm diseases in swine, particularly those associated with highly pathogenic viruses such as African swine fever virus (ASFV) and porcine reproductive and respiratory syndrome virus (PRRSV), inflict devastating economic losses on global pork production. Current control strategies rely heavily on antibiotics and vaccines; however, emerging antimicrobial resistance and vaccine efficacy variability necessitate alternative therapeutic approaches. Traditional Chinese Veterinary Medicine offers potential solutions, yet rigorous evidence-based studies are required to meet modern regulator

From molecular networks to the clinic: a systems biology-nanomedicine roadmap for osteoarthritis diagnosis, regeneration, and safety-by-design.

Osteoarthritis (OA) is a severe, whole-joint illness that is characterized by the permanent destruction of articular cartilage. The failure of traditional therapies and early tissue engineering efforts is mainly due to their reductionist biological strategies and reliance on bulk, non-biomimetic materials that cannot replicate the complex nanoscale architecture of the native extracellular matrix. This review proposes a closed-loop, multidisciplinary roadmap that integrates systems biology and biomimetic nanomedicine to advance OA diagnosis, cartilage regeneration, and nanomaterial safety-by-de…

Окисляющие молекулярные сигнатуры в неизлечимых заболеваниях: систематический обзор комплексных подходов к машинному обучению и системной биологии.

Окисляющий стресс является одним из основных факторов патогенеза иммунных заболеваний в результате его воздействия на клеточный метаболизм, митохондриальную функцию, иммунную сигнализацию и воспалительную травму тканей. Разрушение гомеостазиса способствует метаболическому перепрограммированию и постоянной активации врожденной и адаптивной иммунной реакции, что способствует прогрессированию заболеваний через многочисленные подстрекательские и аутоиммунные расстройства. Последние достижения в области высокопроизводительных молекулярных технологий привели к созданию крупномасштабных многомерных н

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… Second, the study applied computational analytical approaches including machine learning algorithms, bioinformatic analysis, or systems biology methods. … Systems biology approaches have further revealed regulatory networks that connect oxidative stress with immune signaling pathways and metabolic processes. …

A Systems Biology Approach to Memory Health: Integrating Network Pharmacology, Gut Microbiota, and Multi-Omics for Health Functional Foods.

Memory impairment, ranging from mild memory impairment to neurodegenerative diseases such as Alzheimer's disease, poses an escalating global … As, gut microbiota signatures, epigenetic modifications, and neuroactive metabolites. By leveraging systems biology approaches, we explore how network pharmacology, gut-brain axis modulation, and multi-omics integration can help to elucidate the complex interactions between HFF components and memory-related pathways such as neuroinflammation, oxidative stress, sy …

Systems Biology and Functional Assessments of Human iPSC-Cardiomyocyte Models of Insulin Resistance Capture Key Hallmarks of Diabetic Cardiomyopathy.

UNLABELLED: Human-centric models of diabetic cardiomyopathy (DbCM) are needed to provide mechanistic insights and translationally relevant therapeutic targets for patients with diabetes. A systems biology approach using insulin resistant (IR) two-dimensional (2D) human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and three-dimensional (3D) engineered heart tissue (EHT) provides a comprehensive evaluation of dysregulated pathways and determines suitability as a translationally relevant model of DbCM. Culturing hiPSC-CMs in 2D or 3D EHT in IR media induced insulin resistance …

Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction.

The cultivated meat industry, also known as cell-based meat, cultured meat, lab-grown meat, or meat alternatives, is a growing field that aims to generate animal tissues ex-vivo in a cost-effective manner that achieves price parity with traditional agricultural products. However, cell culture media costs account for 55%-90% of production costs. To address this issue, efforts are aimed at optimizing media composition. Systems biology-driven approaches have been successfully used to improve the biomass and productivity of multiple bioproduction platforms, like Chinese hamster ovary cells, by acc…

Deciphering the Potential Pharmaceutical Mechanism of GUI-ZHI-FU-LING-WAN on Systemic Sclerosis based on Systems Biology Approaches.

Systemic sclerosis (SSc; scleroderma) is a complicated idiopathic connective tissue disease with seldom effective treatment. GUI-ZHI-FU-LING … n in macrophages, which is consistent with previous conclusion that GFW is able to relieve SSc. The systems biology approach provides a new insight for deepening understanding about TCM.

Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes.

Solid organ transplantation (SOT) outcomes have continued to improve, although long-term use of immunosuppressants can lead to complications such as diabetes, compromising post-transplant outcomes. In this study, we have characterized the intestinal microbiome (IM) composition at the metagenomic level in the context of hyperglycemia induced by immunosuppressants. Sprague-Dawley rats were subjected to doses of tacrolimus and sirolimus that reliably induce hyperglycemia and an insulin-resistant state. Subsequent exposure to probiotics resulted in reversal of hyperglycemia. 16S rRNA and metagenom

Rationale and Design of Family-Based Approach in a Minority Community Integrating Systems-Biology for Promotion of Health (FAMILIA).

BACKGROUND: The 2020 American Heart Association Impact Goal aims to improve cardiovascular health of all Americans by 20% while reducing deaths from cardiovascular disease and stroke by 20%. A large step toward this goal would be to better understand and take advantage of the significant intersection between behavior and biology across the entire life-span. In the proposed FAMILIA studies, we aim to directly address this major knowledge and clinical health gap by implementing an integrated family-centric health promotion intervention and focusing on the intersection of environment and behavior