BrainBase: a curated knowledgebase for brain diseases

DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders

In response to the shortcomings in data quality and coverage for neurological and psychiatric disorders (NPDs) in existing comprehensive databases, this paper introduces the DTNPD database, specifically designed for NPDs. DTNPD contains detailed information on 30 NPDs types, 1847 drugs, 514 drug targets, 64 drug combinations, and 61 potential target combinations, forming a network with 2389 drug-target associations. The database is user-friendly, offering open access and downloadable data, which is crucial for network pharmacology studies. The key strength of DTNPD lies in its robust networks of drug and target combinations, as well as drug-target networks, facilitating research and development in the field of NPDs. The development of the DTNPD database marks a significant milestone in understanding and treating NPDs. For accessing the DTNPD database, the primary URL is http://dtnpd.cnsdrug.com, complemented by a mirror site available at http://dtnpd.lyhbio.com.

Network pharmacology on mechanistic role of Thymus linearis Benth. against gastrointestinal and neurological diseases

BACKGROUND

Thymus linearis Benth. (TL) is native to the Himalayas and has been used traditionally to cure various diseases. Thymus is a well-known aromatic perennial herb commonly known as Van ajwain or Himalayan Thyme. The main components of the TL essential oil are thymol, terpinene, and p-cymene. There are many biological properties that TL has been reported to exhibit, including antioxidant, analgesic, anti-inflammatory, antipyretic, antibacterial, anticancerogenic, and neuroprotective effects.

PURPOSE

In this study, the network pharmacology and molecular docking were used to explore the potential compounds of TL and their interaction mechanism toward gastrointestinal complications and neurological diseases.

METHODS

Network pharmacology was used to analyze the active compounds and protein targets of TL on gastrointestinal and neurological related diseases. Protein-protein interaction and Kyoto Encyclopaedia of Genes and Genomes analysis were used to enrich and evaluate key pathways of target proteins. To ensure the reliability of the network pharmacology prediction estimates, molecular docking was used to confirm the relationships between the core components and targets of TL.

RESULT

77 physiologically active compounds and their 717 predicted protein targets with high association to the neuroactive ligand-receptor interaction pathway were derived from TL. Beta-citronellol, piperitol, p-cymen-8-ol, and alpha-humulene were found to have a role in gastrointestinal diseases associated with neurological diseases. These compounds showed significant levels of multitargeting cluster regulatory activity. The molecular docking results showed regulatory activity of highlighted multi-targeting compounds and the highest docking energy was reported in piperitol.

CONCLUSION

The study shows that Thymus linearis Benth., a medicinal plant with traditional use, possesses valuable biologically active compounds. It emphasizes the potential of Thymus in treating gastrointestinal and neurological diseases by regulating oxidative stress pathways. This research opens up possibilities for discovering antioxidant molecules for future drug development. It is an interesting study with promising implications for further research.

A Network Pharmacology Prediction and Molecular Docking-Based Strategy to Explore the Potential Pharmacological Mechanism of Astragalus membranaceus for Glioma

Glioma treatment in traditional Chinese medicine has a lengthy history. Astragalus membranaceus, a traditional Chinese herb that is frequently utilized in therapeutic practice, is a component of many Traditional Chinese Medicine formulas that have been documented to have anti-glioma properties. Uncertainty persists regarding the molecular mechanism behind the therapeutic effects. Based on results from network pharmacology and molecular docking, we thoroughly identified the molecular pathways of Astragalus membranaceus' anti-glioma activities in this study. According to the findings of the enrichment analysis, 14 active compounds and 343 targets were eliminated from the screening process. These targets were mainly found in the pathways in cancer, neuroactive ligand-receptor interaction, protein phosphorylation, inflammatory response, positive regulation of phosphorylation, and inflammatory mediator regulation of Transient Receptor Potential (TRP) channels. The results of molecular docking showed that the active substances isoflavanone and 1,7-Dihydroxy-3,9-dimethoxy pterocarpene have strong binding affinities for the respective targets ESR2 and PTGS2. In accordance with the findings of our investigation, Astragalus membranaceus active compounds exhibit a multicomponent and multitarget synergistic therapeutic impact on glioma by actively targeting several targets in various pathways. Additionally, we propose that 1,7-Dihydroxy-3,9-dimethoxy pterocarpene and isoflavanone may be the main active ingredients in the therapy of glioma.

Inflammatory diseases: Function of LncRNAs in their emergence and the role of mesenchymal stem cell secretome in their treatment

One of the best treatments for inflammatory diseases such as COVID-19, respiratory diseases and brain diseases is treatment with stem cells. Here we investigate the effect of stem cell therapy in the treatment of brain diseases.Preclinical studies have shown promising results, including improved functional recovery and tissue repair in animal models of neurodegenerative diseases, strokes,and traumatic brain injuries. However,ethical implications, safety concerns, and regulatory frameworks necessitate thorough evaluation before transitioning to clinical applications. Additionally, the complex nature of the brain and its intricate cellular environment present unique obstacles that must be overcome to ensure the successful integration and functionality of genetically engineered MSCs. The careful navigation of this path will determine whether the application of genetically engineered MSCs in brain tissue regeneration ultimately lives up to the hype surrounding it.

Utilizing databases for astrocyte secretome research

INTRODUCTION

Astrocytes are the most abundant cell type in the central nervous system (CNS). They play a pivotal role in supporting neuronal function and maintaining homeostasis by releasing a variety of bioactive proteins, collectively known as the astrocyte secretome. Investigating secretome provides insights into the molecular mechanisms underlying astrocyte function and dysfunction, as well as novel strategies to prevent and treat diseases affecting the CNS.

AREAS COVERED

Proteomics databases are a valuable resource for studying the role of astrocytes in healthy and diseased brain function, as they provide information about gene expression, protein expression, and cellular function. In this review, we discuss existing databases that are useful for astrocyte secretome research.

EXPERT OPINION

Astrocyte secretomics is a field that is rapidly progressing, yet the availability of dedicated databases is currently limited. To meet the increasing demand for comprehensive omics data in glia research, developing databases specifically focused on astrocyte secretome is crucial. Such databases would allow researchers to investigate the intricate molecular landscape of astrocytes and comprehend their involvement in diverse physiological and pathological processes. Expanding resources through the development of databases dedicated to the astrocyte secretome may facilitate further advancements in this field.

A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy

INTRODUCTION

Brain tumors are complex and heterogeneous malignancies with significant challenges in diagnosis, prognosis, and therapy. Proteomics, the large-scale study of proteins and their functions, has emerged as a powerful tool to comprehensively investigate the molecular mechanisms underlying brain tumor regulation.

AREAS COVERED

This review explores brain tumors from a proteomic standpoint, highlighting recent progress and insights gained through proteomic methods. It delves into the proteomic techniques employed and underscores potential biomarkers for early detection, prognosis, and treatment planning. Recent PubMed Central proteomic studies (2017-present) are discussed, summarizing findings on altered protein expression, post-translational changes, and protein interactions. This sheds light on brain tumor signaling pathways and their significance in innovative therapeutic approaches.

EXPERT OPINION

Proteomics offers immense potential for revolutionizing brain tumor diagnosis and therapy. To unlock its full benefits, further translational research is crucial. Combining proteomics with other omics data enhances our grasp of brain tumors. Validating and translating proteomic biomarkers are vital for better patient results. Challenges include tumor complexity, lack of curated proteomic databases, and the need for collaboration between researchers and clinicians. Overcoming these challenges requires investment in technology, data sharing, and translational research.

Integrated analysis of robust sex-biased gene signatures in human brain

BACKGROUND

Sexual dimorphism is highly prominent in mammals with many physiological and behavioral differences between male and female form of the species. Accordingly, the fundamental social and cultural stratification factors for humans is sex. The sex differences are thought to emerge from a combination of genetic and environmental factors. It distinguishes individuals most prominently on the reproductive traits, but also affects many of the other related traits and manifest in different disease susceptibilities and treatment responses across sexes. Sex differences in brain have raised a lot of controversy due to small and sometimes contradictory sex-specific effects. Many studies have been published to identify sex-biased genes in one or several brain regions, but the assessment of the robustness of these studies is missing. We therefore collected huge amount of publicly available transcriptomic data to first estimate whether consistent sex differences exist and further explore their likely origin and functional significance.

RESULTS AND CONCLUSION

In order to systematically characterise sex-specific differences across human brain regions, we collected transcription profiles for more than 16,000 samples from 46 datasets across 11 brain regions. By systematic integration of the data from multiple studies, we identified robust transcription level differences in human brain across to identify male-biased and female-biased genes in each brain region. Firstly, both male and female-biased genes were highly conserved across primates and showed a high overlap with sex-biased genes in other species. Female-biased genes were enriched for neuron-associated processes while male-biased genes were enriched for membranes and nuclear structures. Male-biased genes were enriched on the Y chromosome while female-biased genes were enriched on the X chromosome, which included X chromosome inactivation escapees explaining the origins of some sex differences. Male-biased genes were enriched for mitotic processes while female-biased genes were enriched for synaptic membrane and lumen. Finally, sex-biased genes were enriched for drug-targets and more female-biased genes were affected by adverse drug reactions than male-biased genes. In summary, by building a comprehensive resource of sex differences across human brain regions at gene expression level, we explored their likely origin and functional significance. We have also developed a web resource to make the entire analysis available for the scientific community for further exploration, available at https://joshiapps.cbu.uib.no/SRB_app/.

Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing four-dimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on timsTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.

Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits

A broad range of complex phenotypes are related to dysfunctions in brain (hereafter referred to as brain-related traits), including various mental and behavioral disorders and diseases of the nervous system. These traits in general share overlapping symptoms, pathogenesis, and genetic components. Here, we present Brain Catalog (https://ngdc.cncb.ac.cn/braincatalog), a comprehensive database aiming to delineate the genetic components of more than 500 GWAS summary statistics datasets for brain-related traits from multiple aspects. First, Brain Catalog provides results of candidate causal variants, causal genes, and functional tissues and cell types for each trait identified by multiple methods using comprehensive annotation datasets (58 QTL datasets spanning 6 types of QTLs). Second, Brain Catalog estimates the SNP-based heritability, the partitioning heritability based on functional annotations, and genetic correlations among traits. Finally, through bidirectional Mendelian randomization analyses, Brain Catalog presents inference of risk factors that are likely causal to each trait. In conclusion, Brain Catalog presents a one-stop shop for the genetic components of brain-related traits, potentially serving as a valuable resource for worldwide researchers to advance the understanding of how GWAS signals may contribute to the biological etiology of brain-related traits.