Cellular Interactions Research Articles

Collagen-targeted protein nanomicelles for the imaging of non-alcoholic steatohepatitis

In vivo molecular imaging tools hold immense potential to drive transformative breakthroughs by enabling researchers to visualize cellular and molecular interactions in real-time and/or at high resolution. These advancements will facilitate a deeper understanding of fundamental biological processes and their dysregulation in disease states. Here, we develop and characterize a self-assembling protein nanomicelle called collagen type I binding – thermoresponsive assembled protein (Col1-TRAP) that binds tightly to type I collagen in vitro with nanomolar affinity. For ex vivo visualization, Col1-TRAP is labeled with a near-infrared fluorescent dye (NIR-Col1-TRAP). Both Col1-TRAP and NIR-Col1-TRAP display approximately a 3.8-fold greater binding to type I collagen compared to TRAP when measured by surface plasmon resonance (SPR). We present a proof-of-concept study using NIR-Col1-TRAP to detect fibrotic type I collagen deposition ex vivo in the livers of mice with non-alcoholic steatohepatitis (NASH). We show that NIR-Col1-TRAP demonstrates significantly decreased plasma recirculation time as well as increased liver accumulation in the NASH mice compared to mice without disease over 4 hours. As a result, NIR-Col1-TRAP shows potential as an imaging probe for NASH with in vivo targeting performance after injection in mice. Statement of significanceDirect molecular imaging of fibrosis in NASH patients enables the diagnosis and monitoring of disease progression with greater specificity and resolution than do elastography-based methods or blood tests. In addition, protein-based imaging probes are more advantageous than alternatives due to their biodegradability and scalable biosynthesis. With the aid of computational modeling, we have designed a self-assembled protein micelle that binds to fibrillar and monomeric collagen in vitro. After the protein was labeled with near-infrared fluorescent dye, we injected the compound into mice fed on a NASH diet. NIR-Col1-TRAP clears from the serum faster in these mice compared to control mice, and accumulates significantly more in fibrotic livers.This work advances the development of targeted protein probes for in vivo fibrosis imaging.

Mapping cellular interactions from spatially resolved transcriptomics data.

Cell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently through the introduction of spatially resolved transcriptomics (SRT) technologies, especially those that achieve single-cell resolution. Nevertheless, substantial challenges remain to analyze such highly complex data properly. Here, we introduce a multiple-instance learning framework, Spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight Spacia's power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates and, most importantly, the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of Spacia for three commercialized single-cell resolution SRT technologies: MERSCOPE/Vizgen, CosMx/NanoString and Xenium/10x. Overall, Spacia represents a notable step in advancing quantitative theories of cellular communications.

Single-Nucleus RNA-Sequencing Reveals a MET+ Oligodendrocyte Subpopulation That Promotes Proliferation of Radiation-Induced Gliomas

PurposeRadiation-induced gliomas (RIGs) are fatal late complications of radiotherapy, with a median survival time of 6–11 months. RIGs demonstrate unique molecular landscape and may originate from a glial lineage distinct from that of primary malignancies or diffuse midline gliomas (DMGs). This study aimed to explore the intratumoral diversity within RIGs to uncover their cellular origin and characteristics, and enhance our understanding of this uncommon tumor type. Methods and MaterialsFormalin-fixed, paraffin-embedded samples were collected from two RIGs and two DMGs for single-nucleus RNA sequencing. A detailed analysis was conducted to assess intratumoral heterogeneity and cellular interactions, including gene set enrichment, pseudotime trajectory, and cell communication analyses. Immunofluorescence staining, proliferation assay, and RNA-seq analysis were also applied to validate our findings. ResultsOur analysis revealed distinct heterogeneity in oligodendrocytes between the DMG and RIG samples. A unique subpopulation of oligodendrocytes in RIGs, which was characterized by gene encoding mesenchymal-epithelial transition factor (c-MET) and therefore termed MET+ ODs, exhibited characteristics typical of cancer cells, such as increased mitotic activity, cancer-related gene expression, and extensive copy number variations. Cell communication studies indicated that MET+ ODs interact vigorously with G1/S and G2/M cycling cells via the neural cell adhesion molecule (NCAM) signaling pathway, potentially enhancing the proliferation of cycling malignant cells. Integrating our results with existing RNA-seq data further supported our hypothesis. The presence of MET+ ODs in RIGs was confirmed by immunostaining, and activation of the NCAM signaling pathway in vitro significantly promoted the proliferation of RIG tumor cells. Moreover, in-vitro radiation induced the transformation of oligodendrocytes to be more similar to MET+ ODs. ConclusionsRIGs are characterized by an oligodendrocyte composition distinct from that of DMGs. A specific subpopulation of MET+ ODs in RIGs may be crucial in tumorigenesis and promote the growth of malignant cells. Identifying MET+ ODs offers a valuable target for future clinical surveillance and therapeutic strategies.

Elastic interactions compete with persistent cell motility to drive durotaxis

Many animal cells that crawl on extracellular substrates exhibit durotaxis, i.e., directed migration toward stiffer substrate regions. This has implications in several biological processes including tissue development and tumor progression. Here, we introduce a phenomenological model for single-cell durotaxis that incorporates both elastic deformation-mediated cell-substrate interactions and the stochasticity of cell migration. Our model is motivated by a key observation in an early demonstration of durotaxis: a single, contractile cell at a sharp interface between a softer and a stiffer region of an elastic substrate reorients and migrates toward the stiffer region. We model migrating cells as self-propelling, persistently motile agents that exert contractile traction forces on their elastic substrate. The resulting substrate deformations induce elastic interactions with mechanical boundaries, captured by an elastic potential. The dynamics is determined by two crucial parameters: the strength of the cellular traction-induced boundary elastic interaction (A), and the persistence of cell motility (Pe). Elastic forces and torques resulting from the potential orient cells perpendicular (parallel) to the boundary and accumulate (deplete) them at the clamped (free) boundary. Thus, a clamped boundary induces an attractive potential that drives durotaxis, while a free boundary induces a repulsive potential that prevents antidurotaxis. By quantifying the steady-state position and orientation probability densities, we show how the extent of accumulation (depletion) depends on the strength of the elastic potential and motility. We compare and contrast crawling cells with biological microswimmers and other synthetic active particles, where accumulation at confining boundaries is well known. We define metrics quantifying boundary accumulation and durotaxis, and present a phase diagram that identifies three possible regimes: durotaxis, and adurotaxis with and without motility-induced accumulation at the boundary. Overall, our model predicts how durotaxis depends on cell contractility and motility, successfully explains some previous observations, and provides testable predictions to guide future experiments.

Efficient Elimination of mtDNA from Mammalian Cells with 2',3'-Dideoxycytidine.

Mammalian cell lines devoid of mitochondrial DNA (mtDNA) are indispensable in studies aimed at elucidating the contribution of mtDNA to various cellular processes or interactions between nuclear and mitochondrial genomes. However, the repertoire of tools for generating such cells (also known as rho-0 or ρ0 cells) remains limited, and approaches remain time- and labor-intensive, ultimately limiting their availability. Ethidium bromide (EtBr), which is most commonly used to induce mtDNA loss in mammalian cells, is cytostatic and mutagenic as it affects both nuclear and mitochondrial genomes. Therefore, there is growing interest in new tools for generating ρ0 cell lines. Here, we examined the utility of 2',3'-dideoxycytidine (ddC, zalcitabine) alone or in combination with EtBr for generating ρ0 cell lines of mouse and human origin as well as inducing the ρ0 state in mouse/human somatic cell hybrids. We report that ddC is superior to EtBr in both immortalized mouse fibroblasts and human 143B cells. Also, unlike EtBr, ddC exhibits no cytostatic effects at the highest concentration tested (200 μM), making it more suitable for general use. We conclude that ddC is a promising new tool for generating mammalian ρ0 cell lines.

Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows

Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ∼3500 proteins at a spatial resolution of 50 μm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.

The dynamics of the metastatic niche: Lung alveolar type 2 cell reprogramming and cancer cell stemness

The complex cellular interactions supporting metastasis formation remain incompletely understood. In this issue of Developmental Cell, Rodrigues etal. describe a positive feedback loop within the lung metastatic niche, whereby disseminated cancer cells promote the multilineage potential of alveolar type 2 cells, favoring cancer cell stemness and metastasis initiation.

Abstract 01: Spatial Transcriptomics Reveals How Smooth Muscle Cells Transform to Renin-Expressing Cells During Homeostatic Challenge

Introduction: Juxtaglomerular (JG) cells sense changes in blood pressure through communication with neighboring cells, and/or the sympathetic nervous system upon which they release renin to maintain homeostasis. To meet the demands for circulating renin when homeostasis is threatened, smooth muscle cells (SMCs) of the renal arterioles are transformed to renin-synthesizing cells. Discriminating transformed cells versus JG cells using sorting and scRNA-seq is cumbersome, limiting our ability to explore the events underlying such transformation. Therefore, there is a need to study these cells in situ to assign and determine which epigenomic and cell communication pathways regulate renin expression and SMC transformation. Hypothesis: Transformation of SMCs to renin-expressing cells during homeostatic stress requires specific signals from neighboring cells in addition to intrinsic transcriptomic changes. Methods: A pilot study was performed using two three-month-old C57BL/6 mice fed either a normal diet, or a low-salt diet with the RAS inhibitor, captopril, to induce homeostatic stress. After one week, the kidneys were harvested and prepared for the 10X Genomics Visium platform. Sequencing results were preprocessed using the Space Ranger pipeline (v. 2.0.1) with the mouse mm10 genome prior to downstream analysis using the R packages Seurat, Signac, and CellChat. Results: Homeostatic challenge significantly increased Ren1 expression ( p Holm-adj. =4.63x10 -10 ) and led to more and stronger cellular interactions. Interstitial cells and JG cells contributed the largest percent increase in the observed signaling changes (6.5% and 4.5% respectively). Increased signals for collagen, amyloid precursor protein, osteopontin, laminin, thrombospondin 1, vascular endothelial growth factor, and growth arrest specific pathways drove changes between native and transformed renin-expressing cells. In addition to the established JG cell markers Ren1 and Akr1b7 , transformed cells had significantly increased expression ( p Bonferroni-adj < 0.01) of Hmgcs2 , Cyp4a14 , Suox , Acta2 , Slc2a5 , Ptp4a3 , Sncg , and Rad21 . Conclusions: In conclusion, spatial transcriptomics revealed the evolution of SMC transformation into renin phenotypes by uncovering pathways and genes understudied in the context of renin regulation. Future work will leverage higher resolution spatial technology and further explore the contribution of identified pathways to renin regulation and SMC transformation.

Brain organoids: A new tool for modelling of neurodevelopmental disorders.

Neurodevelopmental disorders are mostly studied using mice as models. However, the mouse brain lacks similar cell types and structures as those of the human brain. In recent years, emergence of three-dimensional brain organoids derived from human embryonic stem cells or induced pluripotent stem cells allows for controlled monitoring and evaluation of early neurodevelopmental processes and has opened a window for studying various aspects of human brain development. However, such organoids lack original anatomical structure of the brain during maturation, and neurodevelopmental maturation processes that rely on unique cellular interactions and neural network connections are limited. Consequently, organoids are difficult to be used extensively and effectively while modelling later stages of human brain development and disease progression. To address this problem, several methods and technologies have emerged that aim to enhance the sophisticated regulation of brain organoids developmental processes through bioengineering approaches, which may alleviate some of the current limitations. This review discusses recent advances and application areas of human brain organoid culture methods, aiming to generalize optimization strategies for organoid systems, improve the ability to mimic human brain development, and enhance the application value of organoids.

ScRNA-seq revealing the molecular atlas of the goat follicular microenvironment over the time course of ovulation

Ovulation is paramount for female animal fertility, necessitating a thorough understanding of its process and molecular underpinnings. This study aimed to delineate the goat ovary temporal dynamics of ovulation. Utilizing single-cell sequencing, we analyzed follicular fluid samples obtained at 0, 6, 12, 18, and 24 h post-hCG administration, identifying 4 cell types and 6 myeloid cell subtypes. We elucidated gene expression and functional changes in granulosa cells over the time course of ovulation. Notably, our study detected and confirmed immune cell infiltration at 6 h post-LH peak. Additionally, we observed significant cellular interactions between granulosa cells and macrophages, with granulosa cells expressing IL1RAP, COL4A1, COL4A2 implicated in immune cell regulation, while macrophages expressed EREG to facilitate oocyte maturation. Collectively, our investigation has established a comprehensive single-cell transcriptome atlas of the ovulating goat ovary for advancing exploration into ovulation mechanisms and developing therapies for ovulatory disorders.

Abstract P176: Elevated Circulating T Cell-Monocyte Complexes in Long COVID-19 Tachycardia Syndrome: Implications of Immune Dysregulation, Inflammation, and Disease Progression

Background: Postural orthostatic tachycardia syndrome (POTS) is a common complication in Long-COVID. Long-COVID POTS (LCP) is characterized by abnormal orthostatic tachycardia, symptoms of orthostatic intolerance, and persistent inflammation. Hypothesis: Novel parameters of immune activation exist in and likely contribute to the pathogenesis of LCP. Methods: We enrolled 15 LCP patients and 5 subjects who recovered from COVID-19 infection without lingering effects as controls. Hemodynamic parameters were measured at baseline and during a 10-minute 75° head-up tilt. Flow cytometry was used to detect circulating T cells, monocyte subsets, and their cytokines. Immune synapse formation between T cells and monocytes was detected using Forster Resonance Energy Transfer (FRET) between T cell receptors (TCR) and human leukocyte antigens (HLAs). Intracellular staining was used to detect the cytokines IL-17A, IFN-γ and IL-6. Results: Subjects with LCP exhibited a greater increase in heart rate (HR) during 10-min upright tilt compared with controls (50.23± 4.6 vs. 20.33 ± 3.17 bpm, p<0.01, Figure). Circulating monocyte/T cell complexes were increased in LCP vs controls and these exhibited high TCR/HLA FRET ( p<0.005 ), suggesting immune synapse formation. Importantly, complexed T cells demonstrated higher levels of IL-17A and IFN-γ, compared to non-complexed T cells and a profound increase in intracellular IL-6 compared to non-complexed monocytes ( p<0.005 ). Notably, the percent of IFN-γ + and IL-17A + T cells in the monocyte/T cell complexes of LCP subjects positively correlated with their increase in HR (ΔHR) in 10 min active standing test (Figure). Conclusion: Circulating T cell-monocyte complexes are markedly increased in humans with LPC, and exhibit evidence of functional and dynamic cellular interactions. We propose that these contribute to persistent inflammation and the pathogenesis of autonomic dysfunction in these subjects.

Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research.

Breast cancer is the most prevalent malignant tumor among women with high heterogeneity. Traditional techniques frequently struggle to comprehensively capture the intricacy and variety of cellular states and interactions within breast cancer. As global precision medicine rapidly advances, single-cell RNA sequencing (scRNA-seq) has become a highly effective technique, revolutionizing breast cancer research by offering unprecedented insights into the cellular heterogeneity and complexity of breast cancer. This cutting-edge technology facilitates the analysis of gene expression profiles at the single-cell level, uncovering diverse cell types and states within the tumor microenvironment. By dissecting the cellular composition and transcriptional signatures of breast cancer cells, scRNA-seq provides new perspectives for understanding the mechanisms behind tumor therapy, drug resistance and metastasis in breast cancer. In this review, we summarized the working principle and workflow of scRNA-seq and emphasized the major applications and discoveries of scRNA-seq in breast cancer research, highlighting its impact on our comprehension of breast cancer biology and its potential for guiding personalized treatment strategies.

Cervical cancer-produced neuromedin-B reprograms Schwann cells to initiate perineural invasion

Perineural invasion (PNI) is a new approach of cervical cancer invasion and metastasis, involving the cross-talk between tumor and nerve. However, the initiating signals and cellular interaction mechanisms of PNI remain largely elusive. The nerve-sparing radical hysterectomy (NSRH) proposed to improve postoperative quality of life is only applicable to cervical cancer patients without PNI. Therefore, it is important to elucidate the underlying mechanisms initiating PNI, and suggest the effective biomarkers to predict PNI before NSRH surgery. Here, we found that PNI is the characteristic of advanced cervical cancer, and Schwann cells were the antecedent cells that initiating PNI. Further, neuropeptide neuromedin B (NMB) produced by cervical cancer cells was determined to induce PNI by reprogramming Schwann cells, including driving their morphological and transcriptional changes, promoting their proliferation and migration, and initiating PNI by secreting CCL2 and directing axon regeneration. Mechanistically, cervical cancer cells-produced NMB activated its receptor NMBR in Schwann cells, and opened the T-type calcium channels to stimulate Ca2+ influx through PKA signaling, which could be blocked by the inhibitor. Clinically, combined examination of serum NMB and CCL2 levels was suggested to effectively predict PNI in cervical cancer patients. Our data demonstrate that cervical cancer-produced NMB initiates the reprograming of Schwann cells, which then direct axon regeneration, thus causing PNI onset. The elevated serum NMB and CCL2 levels may be useful for the decision-making to nerve sparing during hysterectomy surgery of cervical cancer patients.

Age Dependent Integration of Cortical Progenitors Transplanted at the Adult CSF-Brain Interface.

There has been renewed interest in neural transplantation of cells and tissues for brain repair. Recent studies have demonstrated the ability of transplanted neural precursor cells and in vitro grown organoids to mature and locally integrate into host brain neural circuitry. Much effort has focused on how the transplant behaves and functions after the procedure, but the extent to which the host brain can properly innervate the transplant, particularly in the context of aging, is largely unexplored. Here we report that transplantation of rat embryonic cortical precursor cells into the cerebrospinal fluid-subventricular zone (CSF-SVZ) of adult rat brains generates a brain-like tissue (BLT) at an ectopic site. This model allows for the assessment of long-range connectivity and cellular interactions between the transplant and the host brain as a function of host age. The transplanted precursor cells initially proliferate, then differentiate, and develop into mature BLTs, which receive supportive cellular components from the host including blood vessels, microglia, astrocytes, and oligodendrocytes. There was integration of the BLT into the host brain which occurred at all ages studied, suggesting that host age does not affect the maturation and integration of the transplant-derived BLT. Long-range axonal projections from the BLT into the host brain were robust throughout the different aged recipients. However, long-distance innervation originating from the host brain into the BLT significantly declined with age. This work demonstrates the feasibility and utility of integrating new neural tissue structures at ectopic sites into adult brain circuits to study host-transplant interactions.

Comprehensive study of plasma polymerization parameters on thiol-coated LDPE films for effective fibronectin adsorption targeting biomedical applications

In the realm of biomedical applications, biocompatible materials with optimized surface properties are crucial for facilitating cellular interactions. To attain the perfect balance of these properties, surface modification of non-toxic and stable bulk materials is often required. Within this context, this research aimed to improve the physiochemical and cell-responsive properties of a low-density polyethylene film. This was achieved by depositing thiol-rich coatings using a dielectric barrier discharge plasma reactor operating at medium pressures, with 1-propanethiol serving as polymerization precursor. The study systematically investigated the impact of key plasma polymerization parameters, including DBD chamber pressure, treatment time, and the combination of precursor flow rate and discharge power represented by the Yasuda parameter, to identify optimal plasma processing conditions for the formation of thiol-rich coatings. To characterize the coating thickness, hydrophilicity and surface chemical composition, atomic force microscopy, water contact angle measurements, and X-ray photoelectron spectroscopy were employed. The findings indicated that reducing the chamber pressure to 10 kPa led to more hydrophilic and thicker deposits possessing a higher sulphur content. Deposition time (5 to 15 min) also significantly impacted coating thickness and surface chemistry, where long times increased thickness, but also led to a reduced sulphur and increased oxygen content because of more pronounced etching. The optimal deposition time was therefore set at 10 min resulting in the deposition of dense coatings possessing a high number of sulphur-containing functionalities. The Yasuda parameter (W/FM) analysis demonstrated optimal thiol incorporation in combination with high coating stability at an intermediate W/FM value of 72 MJ/kg. Following the determination of the optimal plasma polymerization parameters, the effectiveness of thiol plasma polymerization and subsequent fibronectin immobilization for enhancing cell adhesion and proliferation was investigated. The thiol-coated substrates were found to exhibit superior protein immobilization, because of the high affinity for protein binding of the available thiol groups. To assess cellular responses, Schwann cells were cultured on uncoated and coated samples before and after fibronectin immobilization. The results revealed a superior cellular response of the thiol-coated samples after fibronectin immobilization, showing the highest cell viability and significantly enhanced cell adhesion and proliferation. Collectively, these results underscore the synergistic effect of thiol plasma polymerization and fibronectin immobilization in promoting the cellular response of LDPE substrates, thus highlighting their potential as a surface modification strategy of biomaterials.

Interplay of co-cultured chimeric adipose and gingival tissues exacerbates inflammatory dysfunction relevant to periodontal and metabolic conditions

Adipose tissue dysfunction is a key feature of metabolic syndrome, which increases the risk of periodontitis, an inflammatory disease induced by bacteria that affects the gingiva and other components of periodontal tissue. Recent studies indicate that molecules from inflamed periodontal tissue contribute to adipose tissue dysfunction. However, the cellular mechanisms and interactions between adipose tissue and gingiva driving the progression of metabolic and periodontal conditions remain unclear. To address this, we developed a chimeric (mouse/human) co-culture tissue model (which identifies the origins of species-specific cytokines) to investigate these interactions. Using tissue-specific functional cells and immunocytes, we constructed equivalents of adipose tissue (ATE) and gingiva (GTE), co-cultivating them under inflammatory conditions induced by bacterial endotoxin, lipopolysaccharide (LPS). Our findings showed that exposure to LPS resulted in a notable reduction in lipid accumulation, GLUT4 expression, and adiponectin secretion in ATE, along with increased macrophage colonies forming around lipid droplets, as well as elevated levels of triglyceride, leptin, and IL-6. In GTE, LPS triggered significant inflammatory responses, characterized by increased macrophage accumulation, elevated COX-2 expression, and heightened secretion of inflammatory cytokines. LPS also reduced epithelial thickness and the expression of keratin 19 and collagen IV, indicating impaired barrier function and gingival integrity. Co-culturing ATE with GTE exacerbated these LPS-induced harmful effects in both tissues. In conclusion, our findings suggest that interplay between gingiva and adipose tissue can intensify the inflammatory and dysfunctional changes caused by LPS. This co-culture tissue model offers a valuable tool for future studies on periodontitis and metabolic syndrome.

Advances in spatial multi-omics in tumors.

Single-cell techniques have convincingly demonstrated that tumor tissue usually contains multiple genetically defined cell subclones with different gene mutation sets as well as various transcriptional profiles, but the spatial heterogeneity of the microenvironment and the macrobiological characteristics of the tumor ecosystem have not been described. For the past few years, spatial multi-omics technologies have revealed the cellular interactions, microenvironment, and even systemic tumor-host interactions in the tumor ecosystem at the spatial level, which can not only improve classical therapies such as surgery, radiotherapy, and chemotherapy but also promote the development of emerging targeted therapies in immunotherapy. Here, we review some emerging spatial omics techniques in cancer research and therapeutic applications and propose prospects for their future development.

METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics

Recent advances in spatial transcriptomics (ST) techniques provide valuable insights into cellular interactions within the tumor microenvironment (TME). However, most analytical tools lack consideration of histological features and rely on matched single-cell RNA sequencing data, limiting their effectiveness in TME studies. To address this, we introduce the Morphology-Enhanced Spatial Transcriptome Analysis Integrator (METI), an end-to-end framework that maps cancer cells and TME components, stratifies cell types and states, and analyzes cell co-localization. By integrating spatial transcriptomics, cell morphology, and curated gene signatures, METI enhances our understanding of the molecular landscape and cellular interactions within the tissue. We evaluate the performance of METI on ST data generated from various tumor tissues, including gastric, lung, and bladder cancers, as well as premalignant tissues. We also conduct a quantitative comparison of METI with existing clustering and cell deconvolution tools, demonstrating METI’s robust and consistent performance.

Synergistic collaboration between AMPs and non-direct antimicrobial cationic peptides

Non-direct antimicrobial cationic peptides (NDACPs) are components of the animal innate immune system. But their functions and association with antimicrobial peptides (AMPs) are incompletely understood. Here, we reveal a synergistic interaction between the AMP AW1 and the NDACP AW2, which are co-expressed in the frog Amolops wuyiensis. AW2 enhances the antibacterial activity of AW1 both in vitro and in vivo, while mitigating the development of bacterial resistance and eradicating biofilms. AW1 and AW2 synergistically damage bacterial membranes, facilitating cellular uptake and interaction of AW2 with the intracellular target bacterial genomic DNA. Simultaneously, they trigger the generation of ROS in bacteria, contributing to cell death upon reaching a threshold level. Moreover, we demonstrate that this synergistic antibacterial effect between AMPs and NDACPs is prevalent across diverse animal species. These findings unveil a robust and previously unknown correlation between AMPs and NDACPs as a widespread antibacterial immune defense strategy in animals.

Gingerol-zinc complex loaded 3D-printed calcium phosphate for controlled release application.

The therapeutic potential of natural medicines in treating bone disorders is well-established. Modifications in formulation or molecular structure can enhance their efficacy. Gingerol, an osteogenic active compound derived from ginger roots (Zingiber officinale), can form metal ion complexes. Zinc (Zn), a trace element that combats bacterial infections and promotes osteoblast proliferation, can be complexed with gingerol to form a G-Zn+2 complex. This study investigates a porous 3D-printed (3DP) calcium phosphate (CaP) scaffold loaded with the G-Zn+2 complex for drug release and cellular interactions. The scaffold is coated with polycaprolactone (PCL) to control the drug release. Diffusion-mediated kinetics results in 50% releaseof the G-Zn+2 complex over 6weeks. The G-Zn+2 complex demonstrates cytotoxicity against MG-63 osteosarcoma cells, indicated by the formation of apoptotic bodies and ruptured cell morphology on the scaffolds. G-Zn+2 PCL-coated scaffolds show a 1.2 ± 0.1-fold increase in osteoblast cell viability, and an 11.6 ± 0.5% increase in alkaline phosphatase compared to untreated scaffolds. Treated scaffolds also exhibit reduced bacterial colonization against Staphylococcus aureus bacteria, highlighting the antibacterial potential of the G-Zn+2 complex. The functionalized 3DP CaP scaffold with the G-Zn+2 complex shows significant potential for enhancing bone regeneration and preventing infections in low-load-bearing applications.