Intercellular Signaling Research Articles

Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling.

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. In this study, a multi-level analysis revealed presence of a diverse array of biologically active molecules encapsulated within MEVs, including neuroactive metabolites, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines, and gamma-aminobutyric acid (GABA). Metaproteomics also unveiled an enrichment of neural-related proteins, mainly the glutamine/glutamate/GABA pathway. MEVs were able to cross epithelial and blood-brain barriers in vitro. RNA-seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. Furthermore, MEVs were able to traverse the intestinal barriers and reach distal organs, including the brain, thereby potentially influencing brain functionality and contributing to mental and behavior.

Exosomal miR-320d promotes angiogenesis and colorectal cancer metastasis via targeting GNAI1 to affect the JAK2/STAT3 signaling pathway

Colorectal cancer is a common malignant tumor, whose growth and metastasis are influenced by numerous factors. MicroRNAs have garnered increasing attention in recent years due to their involvement in tumor development. Exosomes are involved in intercellular signaling and influence tumor development by promoting tumor cell proliferation and metastasis through activation of angiogenesis and other mechanisms. This study aimed to investigate how the exosomes containing miR-320d from colorectal cancer (CRC) cells promote colorectal cancer metastasis by regulating angiogenesis. CRC-derived exosomes containing miR-320d can be transferred to vascular endothelial cells, facilitating their proliferation, invasion, migration, and angiogenesis. By targeting GNAI1, miR-320d in these exosomes reduces GNAI1 levels in endothelial cells, causing more JAK2/STAT3 activation and VEGFA production. This ultimately enhances the migration and angiogenic capacity of vascular endothelial cells. Moreover, CRC patients with high levels of miR-320d in their blood respond better to treatment with bevacizumab. In vivo experiments further proved the role of miR-320d from CRC exosomes in increasing tumor size, blood vessel formation, and the spread of cancer to the liver. In this study, we have demonstrated that exosomal miR-320d promotes cancer cell metastasis and enhances angiogenesis by downregulating GNAI1 expression and enhancing JAK2/STAT3.

Metabolism: a potential regulator of neutrophil fate.

Neutrophils are essential components of the innate immune system that defend against the invading pathogens, such as bacteria, viruses, and fungi, as well as having regulatory roles in various conditions, including tissue repair, cancer immunity, and inflammation modulation. The function of neutrophils is strongly related to their mode of cell death, as different types of cell death involve various cellular and molecular alterations. Apoptosis, a non-inflammatory and programmed type of cell death, is the most common in neutrophils, while other modes of cell death, including NETOsis, necrosis, necroptosis, autophagy, pyroptosis, and ferroptosis, have specific roles in neutrophil function regulation. Immunometabolism refers to energy and substance metabolism in immune cells, and profoundly influences immune cell fate and immune system function. Intercellular and intracellular signal transduction modulate neutrophil metabolism, which can, in turn, alter their activities by influencing various cell signaling pathways. In this review, we compile an extensive body of evidence demonstrating the role of neutrophil metabolism in their various forms of cell death. The review highlights the intricate metabolic characteristics of neutrophils and their interplay with various types of cell death.

Extracellular vesicles and micro-RNAs in liver disease.

Progression of liver disease is dependent on intercellular signaling, including those mediated by extracellular vesicles (EVs). Within these EVs, microRNAs (miRNAs) are packaged to selectively silence gene expression in recipient cells for upregulating or downregulating a specific pathway. Injured hepatocytes secrete EV-associated miRNAs which can be taken up by liver sinusoidal endothelial cells (LSECs), immune cells, hepatic stellate cells (HSCs), and other cell types. In addition, these recipient cells will secrete their own EV-associated miRNAs to propagate a response throughout the tissue and the circulation. In this review, we comment on the implications of EV-miRNAs in the progression of alcohol-associated liver disease (ALD), metabolic dysfunction-associated steatohepatitis (MASH), viral and parasitic infections, liver fibrosis, and liver malignancies. We summarize how circulating miRNAs can be used as biomarkers and the potential of utilizing EVs and miRNAs as therapeutic methods to treat liver disease.

Calcium signaling in tunicate development

A comparative overview is provided of Ca2+ signaling and its potential mechanistic roles during development in tunicates. As background, the review presents an introduction to tunicate taxonomy, and then a general overview of Ca2+ signaling and methods for recording and measuring Ca2+ signals. It then covers the dynamics and implicated mechanisms of Ca2+ signals during different phases of development from oocyte to larva. These include signals arising in the unfertilized oocyte, signals associated with fertilization and meiosis, intercellular signals occurring from early cleavage stages through gastrulation, intercellular signals during organogenesis, and signals associated with early behavior. Comparisons are made among different tunicate species and where relevant to other chordate species. In many tunicate species, Ca2+ currents across the oocyte membrane are present prior to fertilization, and in the appendicularian Oikopleura dioica regular Ca2+ transients have been recorded optically prior to fertilization. Ca2+ signals at this stage have been implicated in pre-fertilization oocyte maturation events. The fertilization transient is the most well-studied Ca2+ signal and is triggered by factors from the sperm, including pivotally a phospholipase C (PLC) isoform that catalyzes the generation of IP3, which elicits release of Ca2+ from the endoplasmic reticulum. Post-fertilization signals are similarly dependent on IP3 signaling and are regulated by cyclin-dependent kinase 1 (Cdk1), and thereby linked to the meiotic divisions required for zygote formation. Ca2+ signals associated with early cleavages through gastrulation arise in blastomeres of the muscle lineage and spread from these in a coordinated fashion to other blastomeres through gap junctions. Post-gastrulation Ca2+ signals begin to show tissue-specificity in their temporal pattern as organogenesis proceeds, likely associated with loss of general gap junction transmission. Once neurulation has occurred, Ca2+ signals arise first in the nervous system and are transmitted synaptically to muscle, while Ca2+ signals arising spontaneously in the epidermis follow a separate temporal pattern. Species differences in the spatiotemporal characteristics of pre- and postgastrulation Ca+2 signals are discussed.

Mechanopharmacology: in vitro techniques to advance drug discovery.

Mechanopharmacology is an emerging interdisciplinary field that investigates drug action using biomechanically appropriate in vitro systems to the relevant (patho)physiology. This review outlines emerging technologies and techniques which aim to bridge the gap between mechanical cues influencing cellular biology and conventional pharmacology. We delve into the impact of mechanopharmacology on drug development in cancers and fibrotic diseases. Mechanical cues such as stretch, stiffness, circadian rhythms, fluid flow, intercellular signalling cascades and cytoskeletal structures can modulate drug interactions with molecular targets with implications for drug discovery and development. Models incorporating mechanopharmacological cues to investigate pharmacokinetics, pharmacodynamics and therapeutic outcomes are outlined. Furthermore, this review discusses innovations in the use of biomaterials and microfluidics to further enable the emulation of the mechanical microenvironment. We advocate for the application of mechanopharmacological considerations to improve the physiological relevance of methods used in the drug discovery pipeline.

Exploring the Potential of BEND7 as an Immunomodulatory Biomarker in Sepsis through Integrative Genomic and Transcriptomic Analysis.

Sepsis is a life-threatening condition driven by a dysregulated immune response to infection. Identifying the genetic factors underlying sepsis pathogenesis remains a major challenge in developing effective treatments. The Summary-data-based Mendelian Randomization method was used to integrate genome-wide association study and expression quantitative trait loci data to identify sepsis-related genes. These genes were intersected with prognostic gene sets from Gene Expression Omnibus transcriptomic datasets and validated using an independent dataset. Comprehensive single-cell RNA sequencing analysis, including cell clustering, differential expression analysis, cell-cell communication mapping, and pseudotime trajectory analysis, was performed to explore the roles of the identified genes within the sepsis microenvironment. Intersection of Summary-data-based Mendelian Randomization and Gene Expression Omnibus gene sets, followed by validation, identified two risk genes and five protective genes as significantly differentially expressed. The risk gene BEND7, predominantly expressed in platelets, was further analyzed using single-cell RNA sequencing, revealing strong interactions with immune cells, particularly monocytes and neutrophils, via the intercellular adhesion molecule signaling pathway. Functional enrichment analysis suggested that BEND7-positive platelets play a role in immune modulation and platelet activation. BEND7 was identified as a platelet-specific gene involved in immune regulation during sepsis. Targeting BEND7-positive platelets may present new therapeutic opportunities in sepsis management.

Procoagulant Platelet Characterization by Measuring Phosphatidylserine Exposure and Microvesicle Release from Human Purified Platelets.

Activated platelets promote coagulation primarily by exposing the procoagulant phospholipid phosphatidylserine (PS) on their outer membrane surfaces and releasing PS-expressing microvesicles that retain the original membrane architecture and cytoplasmic components of their originating cells. The accessibility of phosphatidylserine facilitates the binding of major coagulation factors, significantly amplifying the catalytic efficiency of coagulation enzymes, while microvesicle release acts as a pivotal mediator of intercellular signaling. Procoagulant platelets play a crucial role in clot stabilization during hemostasis, and their increased proportion in the bloodstream correlates with an increased risk of thrombosis. It has also been shown that platelet microvesicles are rich in growth factors that promote wound healing and inflammatory modulation. Analyzing phosphatidylserine exposure and microvesicle release using flow cytometry poses significant challenges due to their small size and the limited number of positive events for markers of interest. Despite considerable advances in the last decade, methods for assessing phosphatidylserine exposure and microvesicle release remain a work in progress. Unfortunately, no single universally applicable protocol exists, and several factors must be evaluated to determine the most appropriate methodology for each specific application. Here, we describe a detailed protocol for isolating washed platelets from human blood, followed by collagen and/or thrombin activation, to measure the exposure of phosphatidylserine and microvesicle release that characterize procoagulant platelets. This protocol is designed to facilitate the initial preparation of platelet-rich plasma and the isolation of washed platelets. Finally, phosphatidylserine exposure and microvesicle release are quantified by flow cytometry, enabling the identification of procoagulant platelets.

Single-cell analysis combined with transcriptome sequencing identifies autophagy hub genes in macrophages after spinal cord injury

Spinal cord injury (SCI) is a neurological disease characterized by the loss of motor and sensory function below the injury level. The pathogenesis of SCI is complex, involving the recruitment of various cells that play key roles in the injury area. Single-cell RNA sequencing (scRNA-seq) can analyze cell heterogeneity and inter-cell communication. Bulk RNA-seq offers advantages such as low cost, mature technology and high throughput. Joint analysis of bulk RNA-seq and scRNA-seqis more complementary for exploring the pathophysiology of diseases. In this study, we revealed changes in cell clusters and intercellular signaling after SCI through the scRNA-seq analysis. Bioinformatics analyses and experimental verification showed that macrophages increase rapidly and become the dominant cell type after SCI. The mTOR gene is the key molecule of M1 macrophage autophagy blockade and the PI3K-AKT-mTOR signaling pathway plays an important role in blockings macrophage autophagy.

Establishment of an Idiosyncratic Drug-Induced Liver Injury Model on a Stacked Array Chip for Identification of CCL5-Mediated Paracrine Dynamics.

Idiosyncratic drug-induced liver injury (iDILI) poses significant challenges in both drug development and clinical practice due to its unpredictable nature and poorly understood mechanism. The current in vitro iDILI models are limited in their ability to replicate dynamic paracrine signaling in the inflammatory microenvironment. Here, we develop an iDILI model on a stacked array chip, allowing ease of assembly and disassembly for precise temporal manipulation of 3D liver microtissue and macrophages. First, the iDILI model is constructed and optimized on the chip to effectively distinguish drugs inducing idiosyncratic versus intrinsic liver injuries. Next, the iDILI mechanism is investigated using nimesulide (NIM) as a case study. Our organ-on-a-chip model successfully recapitulates iDILI, offering a platform to distinguish drugs between intrinsic and idiosyncratic liver injury. Our findings revealed that NIM-induced iDILI triggered inflammation-induced injury in the liver microtissues through activating the TNF pathways. Moreover, NIM-induced iDILI promotes the M1 polarization of macrophages through CCL5-mediated paracrine dynamics, influenced by the interactions between hepatocytes and macrophages. Leveraging the flexibility of the chip, we observe a dynamic equilibrium between preactivation of inflammation and the pretreatment of NIM during iDILI process. Therefore, our developed iDILI model on a stacked array chip provides a valuable tool for identifying iDILI drugs and understanding the importance of temporal specificity in intercellular signaling in iDILI.

TET2 promotes tumor antigen presentation and T cell IFN-γ, which is enhanced by vitamin C.

Immune evasion by tumors is promoted by low T cell infiltration, ineffective T cell activity directed against the tumor, and reduced tumor antigen presentation. The TET2 DNA dioxygenase gene is frequently mutated in hematopoietic malignancies and loss of TET enzymatic activity is found in a variety of solid tumors. We showed previously that vitamin C (VC), a cofactor of TET2, enhances tumor-associated T cell recruitment and checkpoint inhibitor therapy responses in a TET2-dependent manner. Using single-cell RNA sequencing (scRNA-seq) analysis performed on B16-OVA melanoma tumors, we have shown here that an additional function for TET2 in tumors is to promote expression of certain antigen presentation machinery genes, which is potently enhanced by VC. Consistently, VC promoted antigen presentation in cell-based and tumor assays in a TET2-dependent manner. Quantifying intercellular signaling from the scRNA-seq dataset showed that T cell-derived IFN-γ-induced signaling within the tumor and tumor microenvironment requires tumor-associated TET2 expression, which is enhanced by VC treatment. Analysis of patient tumor samples indicated that TET activity directly correlates with antigen presentation gene expression and with patient outcomes. Our results demonstrate the importance of tumor-associated TET2 activity as a critical mediator of tumor immunity, which is augmented by high-dose VC therapy.

A collection of split-Gal4 drivers targeting conserved signaling ligands in Drosophila.

Communication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given this small number of signaling pathways, the existence of multiple related ligands for many of these pathways represents a key evolutionary innovation for encoding complexity into cell-cell signaling. Relatedly, crosstalk between pathways is another critical feature which allows a modest number pathways to ultimately generate an enormously diverse range of outcomes. It would thus be useful to have genetic tools to identify and manipulate not only those cells which express a given signaling ligand, but also those cells that specifically co-express pairs of signaling ligands. We present a collection of split-Gal4 knock-in lines targeting many of the ligands for highly conserved signaling pathways in Drosophila (Notch, Hedgehog, FGF, EGF, TGFβ, JAK/STAT, JNK, and PVR). We demonstrate that these lines faithfully recapitulate the endogenous expression pattern of their targets, and that they can be used to identify cells and tissues that co-express pairs of ligands. As a proof of principle, we demonstrate that the 4th chromosome TGFβ ligands myoglianin and maverick are broadly co-expressed in muscles and other tissues of both larva and adults, and that the JAK/STAT ligands upd2 and upd3 are partially co-expressed from cells of the midgut following gut damage. Together with our previously collection of split-Gal4 lines targeting the seven Wnt ligands, this resource allows Drosophila researchers to identify and genetically manipulate cells that specifically express pairs of conserved ligands from nearly all the major intercellular signaling pathways.

Mechanical forces instruct division plane orientation of cambium stem cells during radial growth in Arabidopsis thaliana

Robust regulation of cell division is central to the formation of complex multi-cellular organisms and is a hallmark of stem cell activity. In plants, due to the absence of cell migration, the correct placement of newly produced cell walls during cell division is of eminent importance for generating functional tissues and organs. In particular, during the radial growth of plant shoots and roots, precise regulation and organization of cell divisions in the cambium are essential to produce adjacent xylem and phloem tissues in a strictly bidirectional manner. Although several intercellular signaling cascades have been identified to instruct tissue organization during radial growth, the role of mechanical forces in guiding cambium stem cell activity has been frequently proposed but, so far, not been functionally investigated on the cellular level. Here, we coupled anatomical analyses with a cell-based vertex model to analyze the role of mechanical stress in radial plant growth at the cell and tissue scale. Simulations based on segmented cellular outlines of radially growing Arabidopsis hypocotyls revealed a distinct stress pattern with circumferential stresses in cambium stem cells, which coincided with the orientation of cortical microtubules. Integrating stress patterns as a cue instructing cell division orientation was sufficient for the emergence of typical cambium-derived cell files and agreed with experimental results for stress-related tissue organization in confining mechanical environments. Our work thus underlines the significance of mechanical forces in tissue organization through self-emerging stress patterns during the growth of plant organs.

Gene Co-Expression Network Analysis Associated with Endometrial Cancer Tumorigenesis and Survival Outcomes.

Endometrial cancer (EC) presents a substantial health challenge, with increasing incidence and mortality rates. Despite advances in diagnosis and treatment, understanding the molecular underpinnings of EC progression remains unknown. In this study, we conducted a comprehensive investigation utilizing The Cancer Genome Atlas (TCGA-UCEC n = 588) data to analyze gene co-expression patterns, elucidate biological process pathways, and identify potential prognostic and diagnostic biomarkers for EC, using weighted gene co-expression network analysis (WGCNA), differential gene expression, survival analysis, and functional analysis, respectively. We determined that the Green module (M5) was significantly correlated with patient survival. Functional analysis of the genes in module M5 indicates involvement in cell cycle regulation, mitotic spindle assembly, and intercellular signaling. TPX2, BUB1, and ESPL1 were among the top differentially expressed genes in the Green module, suggesting their involvement in critical pathways that contribute to disease progression and patient survival outcomes. The biological and clinical assessments of our findings provide an understanding of the molecular landscape of EC and identified several potential prognostic markers for patient risk stratification and treatment selection.

GABAergic signalling in the suprachiasmatic nucleus is required for coherent circadian rhythmicity.

The suprachiasmatic nucleus is the circadian pacemaker of the mammalian brain. Suprachiasmatic nucleus neurons display synchronization of their firing frequency on a circadian timescale, which is required for the pacemaker function of the suprachiasmatic nucleus. However, the mechanisms by which suprachiasmatic nucleus neurons remain synchronized in vivo are poorly understood, although synaptic communication is considered indispensable. Suprachiasmatic nucleus neurons contain the neurotransmitter GABA and express GABA receptors. This has inspired the hypothesis that GABA signalling may play a central role in network synchronization, although this remains untested in vivo. Here, using local genetic deletion, we show that disruption of GABA synaptic transmission within the suprachiasmatic nucleus of adult mice results in the eventual deterioration of physiological and behavioural rhythmicity in vivo and concomitant cellular desynchrony in vitro. These findings suggest that intercellular GABA signalling is essential for behavioural rhythmicity and cellular synchrony of the suprachiasmatic nucleus neural network.

Loss of neuropeptide signalling alters temporal expression of mouse suprachiasmatic neuronal state and excitability.

Individual neurons of the hypothalamic suprachiasmatic nuclei (SCN) contain an intracellular molecular clock that drives these neurons to exhibit day-night variation in excitability. The neuropeptide vasoactive intestinal polypeptide (VIP) and its cognate receptor, VPAC2, are synthesized by SCN neurons and this intercellular VIP-VPAC2 receptor signal facilitates coordination of SCN neuronal activity and timekeeping. How the loss of VPAC2 receptor signalling affects the electrophysiological properties and states of SCN neurons as well as their responses to excitatory inputs is unclear. Here we used patch-clamp electrophysiology and made recordings of SCN neurons in brain slices prepared from transgenic animals that do not express VPAC2 receptors (Vipr2-/- mice) as well as animals that do (Vipr2+/+ mice). We report that while Vipr2+/+ neurons exhibit coordinated day-night variation in their electrical state, Vipr2-/- neurons lack this and instead manifest a range of states during both day and night. Further, at the population level, Vipr2+/+ neurons vary the membrane threshold potential at which they start to fire action potentials from day to night, while Vipr2-/- neurons do not. We provide evidence that Vipr2-/- neurons lack a component of voltage-gated sodium currents that contribute to SCN neuronal excitability. Moreover, we determine that this aberrant temporal control of neuronal state and excitability alters neuronal responses to a neurochemical mimic of the light-input pathway to the SCN. These results highlight the critical role VIP-VPAC2 receptor signalling plays in the temporal expression of individual neuronal states as well as appropriate ensemble activity and input gating of the SCN neural network.

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.

Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology, particularly in early mammalian development, where tissue-level differentiation arises from seemingly cell-autonomous mechanisms. In this study, we present a multi-scale, spatial-stochastic simulation framework for mouse embryogenesis, focusing on inner cell mass (ICM) differentiation into epiblast (EPI) and primitive endoderm (PRE) at the blastocyst stage. Our framework models key regulatory and tissue-scale interactions in a biophysically realistic fashion, capturing the inherent stochasticity of intracellular gene expression and intercellular signaling, while efficiently simulating these processes by advancing event-driven simulation techniques. Leveraging the power of Simulation-Based Inference (SBI) through the AI-driven Sequential Neural Posterior Estimation (SNPE) algorithm, we conduct a large-scale Bayesian inferential analysis to identify parameter sets that faithfully reproduce experimentally observed features of ICM specification. Our results reveal mechanistic insights into how the combined action of autocrine and paracrine FGF4 signaling coordinates stochastic gene expression at the cellular scale to achieve robust and reproducible ICM patterning at the tissue scale. We further demonstrate that the ICM exhibits a specific time window of sensitivity to exogenous FGF4, enabling lineage proportions to be adjusted based on timing and dosage, thereby extending current experimental findings and providing quantitative predictions for both mutant and wild-type ICM systems. Notably, FGF4 signaling not only ensures correct EPI-PRE lineage proportions but also enhances ICM resilience to perturbations, reducing fate-proportioning errors by 10-20% compared to a purely cell-autonomous system. Additionally, we uncover a surprising role for variability in intracellular initial conditions, showing that high gene-expression heterogeneity can improve both the accuracy and precision of cell-fate proportioning, which remains robust when fewer than 25% of the ICM population experiences perturbed initial conditions. Our work offers a comprehensive, spatial-stochastic description of the biochemical processes driving ICM differentiation and identifies the necessary conditions for its robust unfolding. It also provides a framework for future exploration of similar spatial-stochastic systems in developmental biology.

N-Cadherin — A Potential Target for Psychopharmacology

Glycoprotein N-cadherin (Neuronal cadherin) belongs to the family of calcium-dependent cell adhesion molecules, representing a key element that carries out intercellular contacts in brain neurons. However, it is involved not only in the mechanical connection of neurons, but also influences the specifics of the further development and functional state of the neuron. This is due to the active interaction of N-cadherin with many proteins at the pre- and post-synapse, initiating a cascade of reactions that provide such processes as long-term potentiation (underlying learning and memory), morphogenesis, neuronal recognition, activation of receptors (NMDA and AMPA types), regulation of cytoskeleton formation. This polyfunctionality is necessary for specific neurons to connect to each other in a certain way, and such adhesion leads to the coordination of cell behavior through intercellular signaling and spatio–temporal control of differential gene expression. Mutations in the genes responsible for the expression of N-cadherin lead to various disorders of the functional activity of the synapse and the processes of spatial orientation and memory. Thus, involvement in important neuroplastic processes regulating cognitive functions and behavior determines interest in studying the effect of drugs on N-cadherin. In particular, N-cadherin deserves closer consideration by pharmacologists as a potential target in the mechanism of action of various psychoactive substances.

Clinical functional proteomics of intercellular signalling in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) has an atypical, highly stromal tumour microenvironment (TME) that profoundly contributes to its poor prognosis1. Here, to better understand the intercellular signalling between cancer and stromal cells directly in PDAC tumours, we developed a multidimensional proteomic strategy called TMEPro. We appliedTMEPro to profile the glycosylated secreted and plasma membrane proteome of 100 human pancreatic tissue samples to a great depth, define cell type origins and identify potential paracrine cross-talk, especially that mediated through tyrosine phosphorylation. Temporal dynamics during pancreatic tumour progression were investigated in a genetically engineered PDAC mouse model. Functionally, we revealed reciprocal signalling between stromal cells and cancer cells mediated by the stromal PDGFR-PTPN11-FOS signalling axis. Furthermore, we examined the generic shedding mechanism of plasma membrane proteins in PDAC tumours and revealed that matrix-metalloprotease-mediated shedding of the AXL receptor tyrosine kinase ectodomain provides an additional dimension of intercellular signalling regulation in the PDAC TME. Importantly, the level of shed AXL has a potential correlation with lymph node metastasis, and inhibition of AXL shedding and its kinase activity showed a substantial synergistic effect in inhibiting cancer cell growth. In summary, we provide TMEPro, a generically applicable clinical functional proteomic strategy, and a comprehensive resource for better understanding the PDAC TME and facilitating the discovery of new diagnostic and therapeutic targets.

Integrative analysis of single-cell transcriptomic and multilayer signaling networks in glioma reveal tumor progression stage.

Tumor microenvironments (TMEs) encompass complex ecosystems of cancer cells, infiltrating immune cells, and diverse cell types. Intercellular and intracellular signals within the TME significantly influence cancer progression and therapeutic outcomes. Although computational tools are available to study TME interactions, explicitly modeling tumor progression across different cancer types remains a challenge. This study introduces a comprehensive framework utilizing single-cell RNA sequencing (scRNA-seq) data within a multilayer network model, designed to investigate molecular changes across glioma progression stages. The heterogeneous, multilayered network model replicates the hierarchical structure of biological systems, from genetic building blocks to cellular functions and phenotypic manifestations. Applying this framework to glioma scRNA-seq data allowed complex network analysis of different cancer stages, revealing significant ligand‒receptor interactions and key ligand‒receptor-transcription factor (TF) axes, along with their associated biological pathways. Differential network analysis between grade III and grade IV glioma highlighted the most critical nodes and edges involved in interaction rewiring. Pathway enrichment analysis identified four essential genes-PDGFA (ligand), PDGFRA (receptor), CREB1 (TF), and PLAT (target gene)-involved in the Receptor Tyrosine Kinases (RTK) signaling pathway, which plays a pivotal role in glioma progression from grade III to grade IV. These genes emerged as significant features for machine learning in predicting glioma progression stages, achieving 87% accuracy and 93% AUC in a 3-year survival prediction through Kaplan-Meier analysis. This framework provides deeper insights into the cellular machinery of glioma, revealing key molecular relationships that may inform prognosis and therapeutic strategies.