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Topic Review
GATNNCDA
Circular RNAs (circRNAs) are a new class of endogenous non-coding RNAs with covalent closed loop structure. Researchers have revealed that circRNAs play an important role in human diseases. As experimental identification of interactions between circRNA and disease is time-consuming and expensive, effective computational methods are an urgent need for predicting potential circRNA–disease associations. In this study, we proposed a novel computational method named GATNNCDA, which combines Graph Attention Network (GAT) and multi-layer neural network (NN) to infer disease-related circRNAs. Specially, GATNNCDA first integrates disease semantic similarity, circRNA functional similarity and the respective Gaussian Interaction Profile (GIP) kernel similarities. The integrated similarities are used as initial node features, and then GAT is applied for further feature extraction in the heterogeneous circRNA–disease graph. Finally, the NN-based classifier is introduced for prediction. The results of fivefold cross validation demonstrated that GATNNCDA achieved an average AUC of 0.9613 and AUPR of 0.9433 on the CircR2Disease dataset, and outperformed other state-of-the-art methods.
  • 613
  • 20 Aug 2021
Topic Review
Parietal Epithelial Cell Behavior
Glomerular parietal epithelial cells (PECs) have been increasingly recognized to have crucial functions. Lineage tracking in animal models showed the expression of a podocyte phenotype by PECs during normal glomerular growth and after acute podocyte injury, suggesting a reparative role of PECs. Conversely, activated PECs are speculated to be pathogenic and comprise extracapillary proliferation in focal segmental glomerulosclerosis (FSGS) and crescentic glomerulonephritis (CrescGN). The reparative and pathogenic roles of PECs seem to represent two sides of PEC behavior directed by the local milieu and mediators. 
  • 613
  • 17 Feb 2023
Topic Review
Inflammation Leads to Skeletal Muscle Wasting in COPD
Inflammation is one of the primary drivers of skeletal muscle wasting in Chronic Obstructive Pulmonary Disease (COPD), through its catabolic effects.
  • 613
  • 18 Aug 2023
Topic Review
Roles of Histone Deacetylase 6 in Physiological Processes
Histone deacetylase 6 (HDAC6), by deacetylation of multiple substrates and association with interacting proteins, regulates many physiological processes that are involved in cancer development and invasiveness such as cell proliferation, apoptosis, motility, epithelial to mesenchymal transition, and angiogenesis. Due to its ability to remove misfolded proteins, induce autophagy, and regulate unfolded protein response, HDAC6 plays a protective role in responses to stress and enables tumor cell survival. 
  • 613
  • 24 Jan 2024
Topic Review
Macrophage lncRNA in Lung Cancer
Ever since RNA sequencing of whole genomes and transcriptomes became available, numerous RNA transcripts without having the classic function of encoding proteins have been discovered. Long non-coding RNAs (lncRNAs) with a length greater than 200 nucleotides were considered as “junk” in the beginning, but it has increasingly become clear that lncRNAs have crucial roles in regulating a variety of cellular mechanisms and are often deregulated in several diseases, such as cancer. Lung cancer is the leading cause of cancer-related deaths and has a survival rate of less than 10%. Immune cells infiltrating the tumor microenvironment (TME) have been shown to have a great effect on tumor development with macrophages being the major cell type within the TME. Macrophages can inherit an inflammatory M1 or an anti-inflammatory M2 phenotype. Tumor-associated macrophages, which are predominantly polarized to M2, favor tumor growth, angiogenesis, and metastasis.
  • 611
  • 29 Sep 2021
Topic Review
Image-Based Annotation of Chemogenomic Libraries for Phenotypic Screening
Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still pose a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, the researchers report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout, in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health, provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.
  • 609
  • 15 Apr 2022
Topic Review
SWI/SNF Complex in Vascular Smooth Muscle Cells
Mature vascular smooth muscle cells (VSMC) exhibit a remarkable degree of plasticity, a characteristic that has intrigued cardiovascular researchers for decades. It has become increasingly evident that the chromatin remodeler SWItch/Sucrose Non-Fermentable (SWI/SNF) complex plays a pivotal role in orchestrating chromatin conformation, which is critical for gene regulation.
  • 606
  • 30 Jan 2024
Topic Review
Tumor-Associated Macrophages in Cervical Cancer
Both clinicopathological and experimental studies have suggested that tumor-associated macrophages (TAMs) play a key role in cervical cancer progression and are associated with poor prognosis in the respects of tumor cell proliferation, invasion, angiogenesis, and immunosuppression. Therefore, having a clear understanding of TAMs is essential in treating this disease. In this entry, the concept and categories of TAMs, the molecules educating TAMs in cervical cancer, the therapy development targeting TAMs, and the expectation for future study in cervical cancer research  will be discussed.
  • 605
  • 29 Mar 2022
Topic Review
Human Immunodeficiency Virus-Related Myocardial Fibrosis
Chronic inflammation is a characteristic feature of cardiovascular diseases (CVD) and considered a contributor to diastolic dysfunction, heart failure, and sudden cardiac death. This can trigger downstream effects that result in the increased release of pro-coagulant, pro-fibrotic, and pro-inflammatory cytokines. Subsequently, this can lead to an enhanced thrombotic state (by platelet activation), endothelial dysfunction, and myocardial fibrosis. Of note, Studies have revealed that myocardial fibrosis is emerging as a mediator of human immunodeficiency virus (HIV)-related CVD. Together, such factors can eventually result in systolic and diastolic dysfunction, and an increased risk for CVD.
  • 605
  • 26 Sep 2022
Topic Review
BRCA1 and Metastasis: Outcome of Defective DNA Repair
BRCA1 has critical functions in accurately repairing double stand breaks in the DNA through a process known as homologous recombination. BRCA1 also has various functions in other cellular processes that safeguard the genome. Thus, mutations or silencing of this tumor suppressor significantly increases the risk of developing breast, ovarian, and other cancers. The objective of this review is to provide significant insights into the mechanisms by which BRCA1 mutations contribute to the metastatic and aggressive nature of the tumor cells. 
  • 602
  • 07 Jan 2022
Topic Review
CGF Biomolecules
Concentrated Growth Factors (CGF) represent new autologous (blood-derived biomaterial), attracting growing interest in the field of regenerative medicine. 
  • 602
  • 24 Jan 2022
Topic Review
Racial Disparity in Quadruple Negative Breast Cancer
Black/African-American (AA) women, relative to their White/European-American (EA) counterparts, experience disproportionately high breast cancer mortality. Central to this survival disparity, Black/AA women have an unequal burden of aggressive breast cancer subtypes, such as triple-negative breast cancer (ER/PR-, HER2-wild type; TNBC). Quadruple negative breast cancer (QNBC), a subgroup of triple negative breast cancer, has emerged as a highly aggressive breast cancer subtype that disproportionately afflicts and impacts Black/African-American (AA) women.
  • 602
  • 30 Sep 2022
Topic Review
MiRNAs in Comparative Osteosarcoma
Osteosarcoma (OS) is a high-grade malignant tumor of bone composed of mesenchymal cells (malignant osteoblasts) that is able to produce an immature woven bone and osteoid matrix. 
  • 601
  • 10 May 2021
Topic Review
MiRNAs Predicting Response to Oesophageal Cancer Treatment
Oesophageal cancer (OC) is the ninth most common cancer worldwide. Patients receive neoadjuvant therapy (NAT) as standard of care, but less than 20% of patients with oesophageal adenocarcinoma (OAC) or a third of oesophageal squamous cell carcinoma (OSCC) patients, obtain a clinically meaningful response. Developing a method of determining a patient’s response to NAT before treatment will allow rational treatment decisions to be made, thus improving patient outcome and quality of life. MicroRNAs are valuable biomarkers of response to NAT in OC. Research is needed to understand the effects different types of chemotherapy and chemoradiotherapy have on the predictive value of microRNAs; studies also require greater standardization in how response is defined. 
  • 601
  • 07 Mar 2022
Topic Review
Paraoxonases in Neurological Disorders
Paraoxonase enzymes serve as an important physiological redox system that participates in the protection against cellular injury caused by oxidative stress. The PON enzyme family consists of three members (PON-1, PON-2, and PON-3) that share a similar structure and location as a cluster on human chromosome 7. These enzymes exhibit anti-inflammatory and antioxidant properties with well-described roles in preventing cardiovascular disease. Perturbations in PON enzyme levels and their activity have also been linked with the development and progression of many neurological disorders and neurodegenerative diseases.
  • 601
  • 27 Apr 2023
Topic Review
SMIFH2 Targets
The discovery of small molecule inhibitor of formin homology 2 domains (SMIFH2) has provided a unique tool to explore formins’ functions from the molecular to the organismal scales. Due to the important pathophysiological roles of formins in eukaryotes, SMIFH2 has been widely used.
  • 601
  • 02 Jun 2023
Topic Review
p38γ MAPK in Physiology and Disease
p38γ MAPK (also called ERK6 or SAPK3) is a family member of stress-activated MAPKs and has common and specific roles as compared to other p38 proteins in signal transduction. In addition to inflammation, p38γ metabolic signaling is involved in physiological exercise and in pathogenesis of cancer, diabetes, and Alzheimer’s disease, indicating its potential as a therapeutic target. p38γphosphorylates at least 19 substrates through which p38γ activity is further modified to regulate life-important cellular processes such as proliferation, differentiation, cell death, and transformation, thereby impacting biological outcomes of p38γ-driven pathogenesis. P38γ signaling is characterized by its unique reciprocal regulation with its specific phosphatase PTPH1 and by its direct binding to promoter DNAs, leading to transcriptional activation of targets including cancer-like stem cell drivers.
  • 597
  • 04 Jul 2023
Topic Review
LncRNAs in Age-Related Macular Degeneration
lncRNAs are a novel class of functional RNA; the landscape of their mutations and variations is small as compared with other ncRNAs, not to mention mRNAs. However, the variability of lncRNA-encoding genes in the pathogenesis of human diseases, especially in cancer, is emerging (reviewed in the work of), but we have not found any association of lncRNA we described in this review with AMD. On the other hand, AMD is reported to associate with mutations in hundreds of genes, often in the form of polymorphisms, which should be considered in experimental studies and projection of therapeutic interventions (reviewed in the work of).
  • 596
  • 06 Sep 2021
Topic Review
Regulation of Angiogenesis by Non-Coding RNAs in Cancer
Non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, have been identified as crucial regulators of various biological processes through epigenetic regulation, transcriptional regulation, and post-transcriptional regulation. Growing evidence suggests that dysregulation and activation of non-coding RNAs are closely associated with tumor angiogenesis, a process essential for tumor growth and metastasis and a major contributor to cancer-related mortality. Therefore, understanding the molecular mechanisms underlying tumor angiogenesis is of utmost importance. Numerous studies have documented the involvement of different types of non-coding RNAs in the regulation of angiogenesis. 
  • 596
  • 22 Jan 2024
Topic Review
Sexual Dimorphisms in Endothelial Cell Functions in PAD
Peripheral artery disease (PAD) is caused by blocked arteries due to atherosclerosis and/or thrombosis which reduce blood flow to the lower limbs. It results in major morbidity, including ischemic limb, claudication, and amputation, with patients also suffering a heightened risk of heart attack, stroke, and death.
  • 595
  • 24 Jan 2024
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