Defining the Akt1 interactome and its role in regulating the cell cycle

Nano-targeted delivery system: a promising strategy of anthocyanin encapsulation for treating intestinal inflammation

Anthocyanins are natural flavonoids derived from plants, widely recognized for their health-promoting effects, specifically to treat inflammatory bowel disease (Crohn's disease and ulcerative colitis). However, certain limitations are associated with their use, including instability, low solubility and permeability, poor gastrointestinal digestion, and low bioavailability. In this review, nano-carriers (e.g., liposome, polymersome, exosome, halloysite nanotubes, dendrimer, and nano-niosome, etc.) were summarized as anthocyanins delivery vehicles to treat inflammatory bowel disease. Recent progress on emerging strategies involved surface functionalization, responsive release, magnetic orientation, and self-assembly aggregation to address intestinal inflammation through nano-carriers and potential mechanisms were discussed. Anthocyanins, water-soluble pigments linked by glycoside bonds have attracted attention to alleviate intestinal inflammation related diseases. Anthocyanins can address intestinal inflammation by exerting their health beneficial effects such as anti-oxidative, anti-inflammatory, regulating the intestinal flora, and promoting apoptosis. Moreover, nano-carriers were discussed as oral delivery system for maximized bioefficacy of anthocyanins and to address concerns related to their low solubility and permeability, poor gastrointestinal metabolism, and low bioavailability were discussed. A future perspective is proposed concerning anthocyanin-loaded nano-carriers, different strategies to improve their efficacy, and developing functional food to treat intestinal inflammation.

GraphkmerDTA: integrating local sequence patterns and topological information for drug-target binding affinity prediction and applications in multi-target anti-Alzheimer's drug discovery

Identifying drug-target binding affinity (DTA) plays a critical role in early-stage drug discovery. Despite the availability of various existing methods, there are still two limitations. Firstly, sequence-based methods often extract features from fixed length protein sequences, requiring truncation or padding, which can result in information loss or the introduction of unwanted noise. Secondly, structure-based methods prioritize extracting topological information but struggle to effectively capture sequence features. To address these challenges, we propose a novel deep learning model named GraphkmerDTA, which integrates Kmer features with structural topology. Specifically, GraphkmerDTA utilizes graph neural networks to extract topological features from both molecules and proteins, while fully connected networks learn local sequence patterns from the Kmer features of proteins. Experimental results indicate that GraphkmerDTA outperforms existing methods on benchmark datasets. Furthermore, a case study on lung cancer demonstrates the effectiveness of GraphkmerDTA, as it successfully identifies seven known EGFR inhibitors from a screening library of over two thousand compounds. To further assess the practical utility of GraphkmerDTA, we integrated it with network pharmacology to investigate the mechanisms underlying the therapeutic effects of Lonicera japonica flower in treating Alzheimer's disease. Through this interdisciplinary approach, three potential compounds were identified and subsequently validated through molecular docking studies. In conclusion, we present not only a novel AI model for the DTA task but also demonstrate its practical application in drug discovery by integrating modern AI approaches with traditional drug discovery methodologies.

Antihepatoma activity of Marsdenia tenacissima polysaccharide-decorated selenium nanoparticles by regulating the Bax/Bcl-2/caspases and p21/Akt/cyclin A2 signaling pathways

Combining selenium nanoparticles (SeNPs) with bioactive polysaccharides is one of the effective ways to overcome the shortcomings of SeNPs and polysaccharides and obtain novel antitumor drug candidates. In this study, a heteropolysaccharide (MTP70) with moderate antihepatoma activity was isolated from the stems of Marsdenia tenacissima (Roxb.) Wight et Arn. To further improve the antihepatoma activity of MTP70 and the application of SeNPs, a novel stable nanoparticle (MTP-SeNP) was designed and fabricated. MTP-SeNPs (Se content of 8.25 %) were characterized as monodisperse spherical nanoparticles (50 nm) with MTP70 wrapped on the surface of the SeNPs by the formation of CO⋯Se bonds and possessed high stability and good dispersion in water for almost a month. In addition, MTP-SeNPs showed higher inhibitory effect compared with MTP70. MTP-SeNPs could effectively inhibit the proliferation, invasion, and metastasis of HepG2 cells by inducing apoptosis and arresting the cell cycle at the S phase, which were closely related to the activation of the Bax/Bcl-2/Caspases and p21/Akt/Cyclin A2 signaling pathways. Our results provide a theoretical basis for further development and application of M. tenacissima polysaccharide, and show that MTP-SeNPs could be explored as a promising anti-hepatoma agent in the pharmaceutical and biomedical industries.

Marein Alleviates Doxorubicin-Induced Cardiotoxicity through FAK/AKT Pathway Modulation while Potentiating its Anticancer Activity

Doxorubicin (DOX) is an effective anticancer agent, yet its clinical utility is hampered by dose-dependent cardiotoxicity. This study explores the cardioprotective potential of Marein (Mar) against DOX-induced cardiac injury and elucidates underlying molecular mechanisms. Neonatal rat cardiomyocytes (NRCMs) and murine models were employed to assess the impact of Mar on DOX-induced cardiotoxicity (DIC). In vitro, cell viability, oxidative stress were evaluated. In vivo, a chronic injection method was employed to induce a DIC mouse model, followed by eight weeks of Mar treatment. Cardiac function, histopathology, and markers of cardiotoxicity were assessed. In vitro, Mar treatment demonstrated significant cardioprotective effects in vivo, as evidenced by improved cardiac function and reduced indicators of cardiac damage. Mechanistically, Mar reduced inflammation, oxidative stress, and apoptosis in cardiomyocytes, potentially via activation of the Focal Adhesion Kinase (FAK)/AKT pathway. Mar also exhibited an anti-ferroptosis effect. Interestingly, Mar did not compromise DOX's efficacy in cancer cells, suggesting a dual benefit in onco-cardiology. Molecular docking studies suggested a potential interaction between Mar and FAK. This study demonstrates Mar's potential as a mitigator of DOX-induced cardiotoxicity, offering a translational perspective on its clinical application. By activating the FAK/AKT pathway, Mar exerts protective effects against DOX-induced cardiomyocyte damage, highlighting its promise in onco-cardiology. Further research is warranted to validate these findings and advance Mar as a potential adjunctive therapy in cancer treatment.

The interaction of mast cells with membranes from lung cancer cells induces the release of extracellular vesicles with a unique miRNA signature

Mast cells (MCs) are immune cells that play roles in both normal and abnormal processes. They have been linked to tumor progression in several types of cancer, including non-small cell lung cancer (NSCLC). However, the exact role of MCs in NSCLC is still unclear. Some studies have shown that the presence of a large number of MCs is associated with poor prognosis, while others have suggested that MCs have protective effects. To better understand the role of MCs in NSCLC, we aimed to identify the initial mechanisms underlying the communication between MCs and lung cancer cells. Here, we recapitulated cell-to-cell contact by exposing MCs to membranes derived from lung cancer cells and confirming their activation, as evidenced by increased phosphorylation of the ERK and AKT kinases. Profiling of the microRNAs that were selectively enriched in the extracellular vesicles (EVs) released by the lung cancer-activated MCs revealed that they contained significantly increased amounts of miR-100-5p and miR-125b, two protumorigenic miRNAs. We explored the pathways regulated by these miRNAs via enrichment analysis using the KEGG database, demonstrating that these two miRNAs regulate p53 signaling, cancer pathways, and pathways associated with apoptosis and the cell cycle.

Embelin targets PI3K/AKT and MAPK in age-related ulcerative colitis: an integrated approach of microarray analysis, network pharmacology, molecular docking, and molecular dynamics

Vaibhdang, an Ayurvedic treatment for Crohn's and UC, has been used for centuries. The main component of Vaibhdang is embelin derived from Embelia ribes. However, the pharmacological and molecular mechanisms of embelin in UC remain unclear. This study investigated the molecular targets and mechanisms of action of embelin in UC using microarray analysis, network pharmacology, molecular docking, and molecular dynamics simulations. Embelin targets were obtained by Swiss Target, TargetNet, STITCH, ChEMBL, and TCMSP. Ulcerative colitis targets were mapped using DisGenNET, Genecards, TCMSP, Therapeutic targets, and GEO databases (GSE87466). Co-targets between ulcerative colitis and embelin were identified, and a PPI network was constructed using the STRING database. To identify the core targets, we used Cytoscape to analyze the topology of the PPI network. There were 545 effective Embelin targets and 5171 effective ulcerative colitis targets, including 1470 DEG targets. ShinyGo and AutoDock were used to analyze GO and KEGG enrichment pathways and docking studies, respectively. Venn diagram analysis revealed 327 core targets of embelin in UC. An enrichment study showed that embelin is involved in PI3K-AKT, MAPK, RAS, and chemokine signalling. The top ten core targets docked with embelin and AKT1, MAPK1, and SRC complexes were utilized as representations and simulated using GROMACS for 100 ns. A comparison of native proteins and their complex interactions with embelin revealed that embelin might act on various PI3K/AKT and MAPK targets to treat ulcerative colitis. This study provides insights into the molecular targets and mechanisms of action of embelin against ulcerative colitis.Communicated by Ramaswamy H. Sarma.

Computer-Aided Identification of Kinase-Targeted Small Molecules for Cancer: A Review on AKT Protein

AKT (also known as PKB) is a serine/threonine kinase that plays a pivotal regulatory role in the PI3K/AKT/mTOR signaling pathway. Dysregulation of AKT activity, especially its hyperactivation, is closely associated with the development of various human cancers and resistance to chemotherapy. Over the years, a wide array of AKT inhibitors has been discovered through experimental and computational approaches. In this regard, herein we present a comprehensive overview of AKT inhibitors identified using computer-assisted drug design methodologies (including docking-based and pharmacophore-based virtual screening, machine learning, and quantitative structure-activity relationships) and successfully validated small molecules endowed with anticancer activity. Thus, this review provides valuable insights to support scientists focused on AKT inhibition for cancer treatment and suggests untapped directions for future computer-aided drug discovery efforts.

Recent advances in the molecular prognostication of meningiomas

Meningiomas are the most common primary intracranial neoplasm. While traditionally viewed as benign, meningiomas are associated with significant patient morbidity, and certain meningioma subgroups display more aggressive and malignant behavior with higher rates of recurrence. Historically, the risk stratification of meningioma recurrence has been primarily associated with the World Health Organization histopathological grade and surgical extent of resection. However, a growing body of literature has highlighted the value of utilizing molecular characteristics to assess meningioma aggressiveness and recurrence risk. In this review, we discuss preclinical and clinical evidence surrounding the use of molecular classification schemes for meningioma prognostication. We also highlight how molecular data may inform meningioma treatment strategies and future directions.

PI3K-AKT-Targeting Breast Cancer Treatments: Natural Products and Synthetic Compounds

Breast cancer is the most commonly diagnosed cancer in women. The high incidence of breast cancer, which is continuing to rise, makes treatment a significant challenge. The PI3K-AKT pathway and its downstream targets influence various cellular processes. In recent years, mounting evidence has shown that natural products and synthetic drugs targeting PI3K-AKT signaling have the potential to treat breast cancer. In this review, we discuss the role of the PI3K-AKT signaling pathway in the occurrence and development of breast cancer and highlight PI3K-AKT-targeting natural products and drugs in clinical trials for the treatment of breast cancer.

CCDC65, a Gene Knockout that leads to Early Death of Mice, acts as a potentially Novel Tumor Suppressor in Lung Adenocarcinoma

CCDC65 is a member of the coiled-coil domain-containing protein family and was only reported in gastric cancer by our group. We first observed that it is downregulated in lung adenocarcinoma based on the TCGA database. Reduced CCDC65 protein was shown as an unfavorable factor promoting the clinical progression in lung adenocarcinoma. Subsequently, CCDC65^-/- mice were found possibly dead of hydrocephalus. Compared with the CCDC65^+/+ mice, the downregulation of CCDC65 in CCDC65^+/- mice significantly increased the formation ability of lung cancer induced by urethane. In the subsequent investigation, we observed that CCDC65 functions as a tumor suppressor repressing cell proliferation in vitro and in vivo. Molecular mechanism showed that CCDC65 recruited E3 ubiquitin ligase FBXW7 to induce the ubiquitination degradation of c-Myc, an oncogenic transcription factor in tumors, and reduced c-Myc binding to ENO1 promoter, which suppressed the transcription of ENO1. In addition, CCDC65 also recruited FBXW7 to degrade ENO1 protein by ubiquitinated modulation. The downregulated ENO1 further reduced the phosphorylation activation of AKT1, which thus inactivated the cell cycle signal. Our data demonstrated that CCDC65 is a potential tumor suppressor by recruiting FBWX7 to suppress c-Myc/ENO1-induced cell cycle signal in lung adenocarcinoma.

NUCKS1 is a highly modified, chromatin-associated protein involved in a diverse set of biological and pathophysiological processes

The Nuclear Casein and Cyclin-dependent Kinase Substrate 1 (NUCKS1) protein is highly conserved in vertebrates, predominantly localized to the nucleus and one of the most heavily modified proteins in the human proteome. NUCKS1 expression is high in stem cells and the brain, developmentally regulated in mice and associated with several diverse malignancies in humans, including cancer, metabolic syndrome and Parkinson's disease. NUCKS1 function has been linked to modulating chromatin architecture and transcription, DNA repair and cell cycle regulation. In this review, we summarize and discuss the published information on NUCKS1 and highlight the questions that remain to be addressed to better understand the complex biology of this multifaceted protein.

Noncanonical HIPPO/MST Signaling via BUB3 and FOXO Drives Pulmonary Vascular Cell Growth and Survival

RATIONALE

The MSTs (mammalian Ste20-like kinases) 1/2 are members of the HIPPO pathway that act as growth suppressors in adult proliferative diseases. Pulmonary arterial hypertension (PAH) manifests by increased proliferation and survival of pulmonary vascular cells in small PAs, pulmonary vascular remodeling, and the rise of pulmonary arterial pressure. The role of MST1/2 in PAH is currently unknown.

OBJECTIVE

To investigate the roles and mechanisms of the action of MST1 and MST2 in PAH.

METHODS AND RESULTS

Using early-passage pulmonary vascular cells from PAH and nondiseased lungs and mice with smooth muscle-specific tamoxifen-inducible Mst1/2 knockdown, we found that, in contrast to canonical antiproliferative/proapoptotic roles, MST1/2 act as proproliferative/prosurvival molecules in human PAH pulmonary arterial vascular smooth muscle cells and pulmonary arterial adventitial fibroblasts and support established pulmonary vascular remodeling and pulmonary hypertension in mice with SU5416/hypoxia-induced pulmonary hypertension. By using unbiased proteomic analysis, gain- and loss-of function approaches, and pharmacological inhibition of MST1/2 kinase activity by XMU-MP-1, we next evaluated mechanisms of regulation and function of MST1/2 in PAH pulmonary vascular cells. We found that, in PAH pulmonary arterial adventitial fibroblasts, the proproliferative function of MST1/2 is caused by IL-6-dependent MST1/2 overexpression, which induces PSMC6-dependent downregulation of forkhead homeobox type O 3 and hyperproliferation. In PAH pulmonary arterial vascular smooth muscle cells, MST1/2 acted via forming a disease-specific interaction with BUB3 and supported ECM (extracellular matrix)- and USP10-dependent BUB3 accumulation, upregulation of Akt-mTORC1, cell proliferation, and survival. Supporting our in vitro observations, smooth muscle-specific Mst1/2 knockdown halted upregulation of Akt-mTORC1 in small muscular PAs of mice with SU5416/hypoxia-induced pulmonary hypertension.

CONCLUSIONS

Together, this study describes a novel proproliferative/prosurvival role of MST1/2 in PAH pulmonary vasculature, provides a novel mechanistic link from MST1/2 via BUB3 and forkhead homeobox type O to the abnormal proliferation and survival of pulmonary arterial vascular smooth muscle cells and pulmonary arterial adventitial fibroblasts, remodeling and pulmonary hypertension, and suggests new target pathways for therapeutic intervention.

Aurora A and AKT Kinase Signaling Associated with Primary Cilia

Dysregulation of kinase signaling is associated with various pathological conditions, including cancer, inflammation, and autoimmunity; consequently, the kinases involved have become major therapeutic targets. While kinase signaling pathways play crucial roles in multiple cellular processes, the precise manner in which their dysregulation contributes to disease is dependent on the context; for example, the cell/tissue type or subcellular localization of the kinase or substrate. Thus, context-selective targeting of dysregulated kinases may serve to increase the therapeutic specificity while reducing off-target adverse effects. Primary cilia are antenna-like structures that extend from the plasma membrane and function by detecting extracellular cues and transducing signals into the cell. Cilia formation and signaling are dynamically regulated through context-dependent mechanisms; as such, dysregulation of primary cilia contributes to disease in a variety of ways. Here, we review the involvement of primary cilia-associated signaling through aurora A and AKT kinases with respect to cancer, obesity, and other ciliopathies.

Transcriptome and Function of Novel Immunosuppressive Autoreactive Invariant Natural Killer T Cells That Are Absent in Progressive Multiple Sclerosis

BACKGROUND AND OBJECTIVE

The aim of this study was to determine whether natural killer T (NKT) cells, including invariant (i) NKT cells, have clinical value in preventing the progression of multiple sclerosis (MS) by examining the mechanisms by which a distinct self-peptide induces a novel, protective invariant natural killer T cell (iNKT cell) subset.

METHODS

We performed a transcriptomic and functional analysis of iNKT cells that were reactive to a human collagen type II self-peptide, hCII707-721, measuring differentially induced genes, cytokines, and suppressive capacity.

RESULTS

We report the first transcriptomic profile of human conventional vs novel hCII707-721-reactive iNKT cells. We determined that hCII707-721 induces protective iNKT cells that are found in the blood of healthy individuals but not progressive patients with MS (PMS). By transcriptomic analysis, we observed that hCII707-721 promotes their development and proliferation, favoring the splicing of full-length AKT serine/threonine kinase 1 (AKT1) and effector function of this unique lineage by upregulating tumor necrosis factor (TNF)-related genes. Furthermore, hCII707-721-reactive iNKT cells did not upregulate interferon (IFN)-γ, interleukin (IL)-4, IL-10, IL-13, or IL-17 by RNA-seq or at the protein level, unlike the response to the glycolipid alpha-galactosylceramide. hCII707-721-reactive iNKT cells increased TNFα only at the protein level and suppressed autologous-activated T cells through FAS-FAS ligand (FAS-FASL) and TNFα-TNF receptor I signaling but not TNF receptor II.

DISCUSSION

Based on their immunomodulatory properties, NKT cells have a potential value in the treatment of autoimmune diseases, such as MS. These significant findings suggest that endogenous peptide ligands can be used to expand iNKT cells, without causing a cytokine storm, constituting a potential immunotherapy for autoimmune conditions, including PMS.

Prediction and Verification of the Major Ingredients and Molecular Targets of Tripterygii Radix Against Rheumatoid Arthritis

Tripterygii Radix exhibits good clinical efficacy and safety in rheumatoid arthritis (RA) patients, but its effective components and mechanism of action are still unclear. The purpose of this study was to explore and verify the major ingredients and molecular targets of Tripterygii Radix in RA using drug-compounds-biotargets-diseases network and protein-protein interaction (PPI) network analyses. The processes and pathways were derived from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The most important compounds and biotargets were determined based on the degree values. RA fibroblast-like synoviocytes (RA-FLS) were separated from RA patients and identified by hematoxylin and eosin (HE) staining and immunohistochemistry. The purity of RA-FLS was acquired by flow cytometry marked with CD90 or VCAM-1. RA-FLS were subjected to control, dimethyl sulfoxide (control), kaempferol, or lenalidomide treatment. Cell migration was evaluated by the transwell assay. The relative expression of biotarget proteins and cytokines was analyzed by western blotting and flow cytometry. In total, 144 chemical components were identified from Tripterygii Radix; kaempferol was the most active ingredient among 33 other components. Fourteen proteins were found to be affected in RA from 285 common biotargets. The tumor necrosis factor (TNF) signaling pathway was predicted to be one of the most latent treatment pathways. Migration of RA-FLS was inhibited and the expression of protein kinase B (AKT1), JUN, caspase 3 (CASP3), TNF receptor 1 and 2 (TNFR1 and TNFR2), interleukin-6 (IL-6), and TNF-α was significantly affected by kaempferol. Thus, this study confirmed kaempferol as the effective component of Tripterygii Radix against RA-FLS and TNF signaling pathway and its involvement in the regulation of AKT1, JUN, CASP3, TNFR1, TNFR2, IL-6, and TNF-α expression.

High Iodine Induces the Proliferation of Papillary and Anaplastic Thyroid Cancer Cells via AKT/Wee1/CDK1 Axis

High iodine can alter the proliferative activity of thyroid cancer cells, but the underlying mechanism has not been fully elucidated. Here, the role of high iodine in the proliferation of thyroid cancer cells was studied. In this study, we demonstrated that high iodine induced the proliferation of BCPAP and 8305C cells via accelerating cell cycle progression. The transcriptome analysis showed that there were 295 differentially expressed genes (DEGs) in BCPAP and 8305C cells induced by high iodine, among which CDK1 expression associated with the proliferation of thyroid cancer cells induced by high iodine. Moreover, the western blot analysis revealed that cells exposed to high iodine enhanced the phosphorylation activation of AKT and the expression of phospho-Wee1 (Ser642), while decreasing the expression of phospho-CDK1 (Tyr15). Importantly, the inhibition of AKT phosphorylation revered the expression of CDK1 induced by high iodine and arrested the cell cycle in the G₁ phase, decreasing the proliferation of thyroid cancer cells induced by high iodine. Taken together, these findings suggested that high iodine induced the proliferation of thyroid cancer cells through AKT-mediated Wee1/CDK1 axis, which provided new insights into the regulation of proliferation of thyroid cancer cells by iodine.

Transcriptome and Differential Methylation Integration Analysis Identified Important Differential Methylation Annotation Genes and Functional Epigenetic Modules Related to Vitiligo

Vitiligo is an pigmentation disorder caused by a variety of pathogenic factors; its main pathophysiological conditions include oxidative stress, immune activation, and genetic background. Additionally, DNA methylation is often associated with the pathogenesis of vitiligo; however, the underlying mechanism remains unknown. In the present study, we used the Human Methylation 850K BeadChip platform to detect DNA methylation changes in the vitiligo melanocytes. We then integrated the results with the transcriptome data of vitiligo melanocytes and lesions to analyse the correlation between differentially methylated levels and differentially expressed genes. The results showed that there was a significant negative correlation between methylation levels and differentially expressed genes. Subsequently, we enriched GO and KEGG based on methylated differentially expressed genes (MDEGs) using R package ClusterProfiler, and the results were closely related to the pathogenesis of vitiligo. In addition, we also constructed a PPI network of MDEGs and excavated three important functional epigenetic modules, involving a total of 12 (BCL2L1, CDK1, ECT2, HELLS, HSP90AA1, KIF23, MC1R, MLANA, PBK, PTGS2, SOX10, and TYRP1) genes. These genes affect melanocyte melanogenesis, cellular oxidative stress and other important biological processes. Our comprehensive analysis results support the significant contribution of the status of DNA methylation modification to vitiligo, which will help us to better understand the molecular mechanism of vitiligo and explore new therapeutic strategies.

Potential therapeutic targets and molecular details of anthocyan-treated inflammatory bowel disease: a systematic bioinformatics analysis of network pharmacology

Anthocyans, containing anthocyanins and anthocyanidins, play a crucial role in preventing and treating inflammatory bowel disease (IBD). Most anthocyanins and their basic elements, namely anthocyanidins have been recognized for the effective treatment of IBD, but the key biomarkers of anthocyan-treated IBD remain unclear. In this study, a bioinformatics analysis based on network pharmacology was performed to demonstrate the core-targets, biological functions, and signaling pathways of most common anthocyanidins that existed in anthocyans to reveal their potential or major mechanisms. The network pharmacology of the multi-target drug molecular design with specific signal nodes was selected, which was used to analyse core targets and complete the bioinformatics analysis of core targets. The network assays indicated 44 common targeted genes, 5 of which were core targets of both six most common anthocyanidins and IBD. These 44 common targets related to major signaling mechanisms of the six most common anthocyanidins in IBD may involve following processes: promotion of intracellular metabolism and proliferation, inhibition of cell necrosis, anti-inflammation and regulation of intestinal epithelial survival mainly via pathways such as, the EGFR tyrosine kinase inhibitor resistance pathway, platelet activation, microRNAs in cancer, arachidonic acid metabolism and the cGMP-PKG signaling pathway. Thus, our findings may provide other molecular details about anthocyans in the treatment of IBD and contribute towards the use of anthocyanidins, which will be meaningful shedding light on the action mechanisms of anthocyanidins in treating IBD.

THP1 proteomics in response to mycobacterium tuberculosis infection

Temporal data on how the mycobacterium infection establishes itself inside the host cell is not available. We differentiated human THP1 cell line with PMA and infected them with different laboratory (H37Ra and H37Rv) and clinical strains (BND433 and JAL2287) of mycobacterium tuberculosis (Mtb). Uninfected differentiated THP1 cells were used as infection control. Host proteome was investigated at four different time points to understand the dynamics of host response to mycobacterial infection with time. The investigated time points included 6 hrs, 18 hrs, 30 hrs and 42 hrs of infection with all the Mtb strains. SWATH-MS method was used to quantitate the host proteome in response to Mtb infection and the data thus obtained are available via PRIDE repository with the dataset identifier PXD022352 (https://www.ebi.ac.uk/pride/archive/projects/PXD022352).

Berberine and Emodin abrogates breast cancer growth and facilitates apoptosis through inactivation of SIK3-induced mTOR and Akt signaling pathway

Salt-inducible kinases 3 (SIK3) belong to the AMPK-related family of kinases, which have been implicated in the regulation of cell metabolism, cell polarity remodelling, and epithelial-mesenchymal transition. Elevated SIK3 expressions in breast cancer cells are shown to contribute to tumorigenesis; however, the underlying mechanism remains to be elucidated. In this study, we demonstrate that SIK3 expression is upregulated and concurrently high expression of SIK3 is associated with poor survival in breast cancer. Specifically, SIK3 knockdown revealed that SIK3 is required for the mTOR/Akt signaling pathway and proliferation of breast cancer cells. Furthermore, our findings showed that Emodin (EMO) combined with Berberine (BBR) significantly inhibited SIK3 activity, leading to reduced cell growth, increased cell cycle arrest and apoptosis in breast cancer cells, but not in non-malignant breast epithelial cell line. Mechanistic studies further reveal that EMO and BBR in combined treatment inhibited SIK3-potentiated mTOR-mediated aerobic glycolysis and cell growth in breast cancer cells. Moreover, combination treatments attenuate Akt signaling, thereby inducing G0/G1 phase cell cycle arrest and apoptosis of breast cancer cells in a SIK3-dependent manner. CRISPR/Cas9 or siRNA-mediated SIK3 knockout/knockdown showed an opposite trend in both the luminal and basal-like breast cancer. Collectively, our findings reveal that combination of EMO and BBR attenuates SIK3-driven tumor growth in breast cancer, and thus, EMO and BBR might be a novel SIK3 inhibitor explored into the prevention of breast cancer.

Targeting Kinase Interaction Networks: A New Paradigm in PPI Based Design of Kinase Inhibitors

BACKGROUND

Kinases are key modulators in regulating diverse range of cellular activities and are an essential part of the protein-protein interactome. Understanding the interaction of kinases with different substrates and other proteins is vital to decode the cell signaling machinery as well as causative mechanism for disease onset and progression.

OBJECTIVE

The objective of this review is to present all studies on the structure and function of few important kinases and highlight the protein-protein interaction (PPI) mechanism of kinases and the kinase specific interactome databases and how such studies could be utilized to develop anticancer drugs.

METHODS

The article is a review of the detailed description of the various domains in kinases that are involved in protein-protein interactions and specific inhibitors developed targeting these PPI domains.

RESULTS

The review has surfaced in depth the interacting domains in key kinases and their features and the roles of PPI in the human kinome and the various signaling cascades that are involved in certain types of cancer.

CONCLUSION

The insight availed into the mechanism of existing peptide inhibitors and peptidomimetics against kinases will pave way for the design and generation of domain specific peptide inhibitors with better productivity and efficiency and the various software and servers available can be of great use for the identification and analysis of protein-protein interactions.

Single-Cell RNA Sequencing of Human Embryonic Stem Cell Differentiation Delineates Adverse Effects of Nicotine on Embryonic Development

Nicotine, the main chemical constituent of tobacco, is highly detrimental to the developing fetus by increasing the risk of gestational complications and organ disorders. The effects of nicotine on human embryonic development and related mechanisms, however, remain poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq) of human embryonic stem cell (hESC)-derived embryoid body (EB) in the presence or absence of nicotine. Nicotine-induced lineage-specific responses and dysregulated cell-to-cell communication in EBs, shedding light on the adverse effects of nicotine on human embryonic development. In addition, nicotine reduced cell viability, increased reactive oxygen species (ROS), and altered cell cycling in EBs. Abnormal Ca2+ signaling was found in muscle cells upon nicotine exposure, as verified in hESC-derived cardiomyocytes. Consequently, our scRNA-seq data suggest direct adverse effects of nicotine on hESC differentiation at the single-cell level and offer a new method for evaluating drug and environmental toxicity on human embryonic development in utero.

Cell Cycle Regulation by Ca2+-Activated K⁺ (BK) Channels Modulators in SH-SY5Y Neuroblastoma Cells

The effects of Ca²⁺-activated K⁺ (BK) channel modulation by Paxilline (PAX) (10⁻⁷–10⁻⁴ M), Iberiotoxin (IbTX) (0.1–1 × 10⁻⁶ M) and Resveratrol (RESV) (1–2 × 10⁻⁴ M) on cell cycle and proliferation, AKT1p^Ser473 phosphorylation, cell diameter, and BK currents were investigated in SH-SY5Y cells using Operetta-high-content-Imaging-System, ELISA-assay, impedentiometric counting method and patch-clamp technique, respectively. IbTX (4 × 10⁻⁷ M), PAX (5 × 10⁻⁵ M) and RESV (10⁻⁴ M) caused a maximal decrease of the outward K⁺ current at +30 mV (Vm) of −38.3 ± 10%, −31.9 ± 9% and −43 ± 8%, respectively, which was not reversible following washout and cell depolarization. After 6h of incubation, the drugs concentration dependently reduced proliferation. A maximal reduction of cell proliferation, respectively of −60 ± 8% for RESV (2 × 10⁻⁴ M) (IC50 = 1.50 × 10⁻⁴ M), −65 ± 6% for IbTX (10⁻⁶ M) (IC50 = 5 × 10⁻⁷ M), −97 ± 6% for PAX (1 × 10⁻⁴ M) (IC50 = 1.06 × 10⁻⁵ M) and AKT1p^ser473 dephosphorylation was observed. PAX induced a G1/G2 accumulation and contraction of the S-phase, reducing the nuclear area and cell diameter. IbTX induced G1 contraction and G2 accumulation reducing diameter. RESV induced G2 accumulation and S contraction reducing diameter. These drugs share common actions leading to a block of the surface membrane BK channels with cell depolarization and calcium influx, AKT1p^ser473 dephosphorylation by calcium-dependent phosphatase, accumulation in the G2 phase, and a reduction of diameter and proliferation. In addition, the PAX action against nuclear membrane BK channels potentiates its antiproliferative effects with early apoptosis.