Distribution Of Cell Populations Research Articles

LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data.

We describe LnCeCell 2.0 (http://bio-bigdata.hrbmu.edu.cn/LnCeCell), an updated resource for lncRNA-associated competing endogenous RNA (ceRNA) networks and web tools based on single-cell and spatial transcriptomics sequencing(stRNA-seq)data. We have updated the LnCeCell 2.0 database with significantly expanded data and improved features, including(i) 257 single-cell RNA sequencingandstRNA-seqdatasets across 86 diseases/phenotypes and 80 human normal tissues, (ii) 836581 cell-specific and spatial spot-specific ceRNA interactions and functional networks for 1002988 cells and 367971 spatial spots, (iii) 15489 experimentally supported lncRNA biomarkers related to disease pathology, diagnosis and treatment, (iv) detailed annotation of cell type, cell state, subcellular and extracellular locations of ceRNAs through manual curationand (v) ceRNA expression profiles and follow-up clinical information of 20326 cancer patients. Further, a panel of 24 flexible tools (including 8 comprehensive and 16 mini-analysis tools) was developed to investigate ceRNA-regulated mechanisms at single-cell/spot resolution. The CeCellTraject tool, for example, illustrates the detailed ceRNA distribution of different cell populations and explores the dynamic change of the ceRNA network along the developmental trajectory. LnCeCell 2.0 will facilitate the study of fine-tuned lncRNA-ceRNA networks with single-cell and spatial spot resolution, helping us to understand the regulatory mechanisms behind complex microbial ecosystems.

Mapping cellular coverage suitability: a GIS-Based approach to identifying poor service areas

Cellular coverage is a critical component of modern telecommunications, providing essential services for communication, commerce, and emergency response. Despite its importance, many regions, particularly those with challenging terrain or low population density, experience inadequate cellular service. This study focuses on the commune of Laghouat, Algeria, employing a GIS-based Multi-Criteria Analysis (MCA) to assess cellular coverage suitability. Using ArcGIS Pro, four key factors were integrated: cell tower locations, terrain elevation, population distribution, and restricted areas. The methodology includes performing a Viewshed analysis to identify dead zones, converting population data into raster format to map demand, and digitizing restricted areas where telecommunication infrastructure development is prohibited. All factors were standardized to a common scale to ensure comparability and a weighted overlay analysis was conducted to generate a comprehensive suitability map. The map highlights areas of poor cellular coverage, guiding the placement of new infrastructure. Additionally, the research considers regulatory restrictions on land use, ensuring compliance with governmental policies. The resulting suitability map provides valuable insights for telecommunications providers and policymakers, enabling them to target underserved regions for infrastructure improvements while adhering to legal constraints. This study offers a robust, scalable framework for identifying and addressing cellular coverage gaps, applicable to other regions with similar geographic and demographic challenges.

Potential of diagnostic electron microscopy of calcification, pathological neovascularization and elastolysis in combination with phenotyping of cell populations in large arteries

Aim. To determine the potential of diagnostic electron microscopy of intraplaque processes (severity of lipid damage, fibrous cap thickness and condition, severity of pathological neovascularization, presence, nature and severity of calcification, ratio and distribution of various cell populations).Material and methods. The study objects were plaques removed during endar­terectomy from the human carotid artery and segments of the human internal mammary artery removed during coronary bypass surgery. Whole specimens were subjected to chemical fixation, staining with heavy metal salts, embedding in epoxy resin followed by layer-by-layer grinding, polishing, contrasting, visualization using back-scattered electron scanning electron microscopy and three-dimensional reconstruction with color mapping (modified EM-BSEM).Results. The use of a modified EM-BSEM made it possible to: 1) visualize the fibrous cap thickness and assess the extracellular matrix; 2) analyze the neointimal lipid distribution; 3) perform three-dimensional reconstruction and analyze the microenvironment of calcifications of various sizes; 4) visualize endothelial cells, defects in interendothelial contacts and the basement membrane of neointimal capillaries with their subsequent three-dimensional reconstruction; 5) perform an analysis of age-dependent defects in the basement membrane and internal elastic membrane of the internal mammary artery. The resolution of the obtained images was significantly superior to intravascular imaging methods (intravascular ultrasound and optical coherence tomography), allowing additional assessment of capillary fluidity, the degree of calcification encapsulation and the condition of elastic fibers. Three-dimensional reconstruction of calcifications, neointimal capillaries and elastic fibers made it possible to assess their spatial density and heterogeneity. Simultaneously with the identification and assessment of these histological structures, objective phenotyping of cell populations was performed, which made it possible to isolate macrophages and foam cells, vascular smooth muscle cells, fibroblasts and endothelial cells in atherosclerotic plaques and automatically identify them through color mapping determined by their electronic contrast distribution signatures.Conclusion. The modified EM-BSEM method allows for universal electron microscopic diagnosis of atherosclerotic and elastolytic lesions of large arteries with high information content about vascular remodeling and high accuracy. Electronic contrast distribution signatures unique for each cell population indicate the possibility of their automated phenotyping using specialized neural network algorithms.

Spatial landscape of malignant pleural and peritoneal mesothelioma tumor immune microenvironment.

Immunotherapies have demonstrated limited clinical efficacy in malignant mesothelioma treatment. We conducted multiplex immunofluorescence (mIF) analyses on tissue microarrays (n=3) from malignant peritoneal (MPeM, n=25) and pleural (MPM, n=88) mesothelioma patients. Our study aimed to elucidate spatial distributions of key immune cell populations and their association with LAG3, BAP1, NF2, and MTAP, with MTAP serving as a CDKN2A/B surrogate marker. Additionally, we examined the relationship between the spatial distribution of major immune cell types with MM patient prognosis and clinical characteristics. We observed a higher degree of interaction between immune cells and tumor cells in MPM compared to MPeM. Notably, within MPM tumors, we detected a significantly increased interaction between tumor cells and CD8+ T cells in tumors with low BAP1 expression compared to those with high BAP1 expression. To support the broader research community, we have developed The Human Spatial Atlas of Malignant Mesothelioma (https://mesotheliomaspatialatlas.streamlit.app/), containing mIF and hematoxylin and eosin (H&E) images.

TME-analyzer: a new interactive and dynamic image analysis tool that identified immune cell distances as predictors for survival of triple negative breast cancer patients

Spatial distribution of intra-tumoral immune cell populations is considered a critical determinant of tumor evolution and response to therapy. The accurate and systemic search for contexture-based predictors would be accelerated by methods that allow interactive visualization and interrogation of tumor micro-environments (TME), independent of image acquisition platforms. To this end, we have developed the TME-Analyzer, a new image analysis tool, which we have benchmarked against 2 software tools regarding densities and networks of immune effector cells using multiplexed immune-fluorescent images of triple negative breast cancer (TNBC). With the TME-Analyzer we have identified a 10-parameter classifier, predominantly featuring cellular distances, that significantly predicted overall survival, and which was validated using multiplexed ion beam time of flight images from an independent cohort. In conclusion, the TME-Analyzer enabled accurate interactive analysis of the spatial immune phenotype from different imaging platforms as well as enhanced utility and aided the discovery of contextual predictors towards the survival of TNBC patients.

Isolating Human Peripheral Blood Mononuclear Cells from Buffy Coats via High Throughput Immunomagnetic Bead Separation.

Peripheral blood mononuclear cells (PBMCs) are a heterogeneous population of monocytes and lymphocytes. Cryopreserved PBMCs have stable viability in long-term storage, making them an ideal cell type for many downstream research purposes, including flow cytometry, immunoassays, and genome sequencing. Typically, PBMCs are isolated viadensity gradient centrifugation, however, it is a low-throughput workflow that is difficult and costly to scale. This article presents a high-throughput workflow using a magnetic bead-based PBMC isolation method that is quick to implement. Total cell concentration, viability, and population distribution with PBMCs obtained using density gradient isolation were compared, and cell viability and proportion of cell types were comparable for both techniques. Isolated PBMCs demonstrated over 70% viability up to 9 days after blood collection, although yield decreased by half after 5 days compared to PBMCs processed within 24 h of collection. In summary, this article describes a PBMC protocol that utilizes a bead-based approach to adapt to a high throughput workflow and demonstrates that both manual and automated bead-based methods can increase processing capacity and provide flexibility for various budgets.

A size-dependent division strategy accounts for leukemia cell size heterogeneity

Heterogeneity in the size distribution of cancer cell populations is linked to drug resistance and invasiveness. However, understanding how such heterogeneity arises is still damped by the difficulties of monitoring the proliferation at the typical timescales of mammalian cells. Here, we show how to infer the growth regime and division strategy of leukemia cell populations using live cell fluorescence labeling and flow cytometry in combination with an analytical model where cell growth and division rates depend on powers of the size. We found that the dynamics of the size distribution of Jurkat T-cells is reproduced by (i) a sizer-like division strategy, with (ii) division times following an Erlang distribution and (iii) fluctuations up to ten percent of the inherited fraction of size at division. Overall, our apparatus can be extended to other cell types and environmental conditions allowing for a comprehensive characterization of the growth and division model different cells adopt.

Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments.

Tumor microenvironments (TMEs) contain vast amounts of information on patient's cancer through their cellular composition and the spatial distribution of tumor cells and immune cell populations. Exploring variations in TMEs between patient groups, as well as determining the extent to which this information can predict outcomes such as patient survival or treatment success with emerging immunotherapies, is of great interest. Moreover, in the face of a large number of cell interactions to consider, we often wish to identify specific interactions that are useful in making such predictions. We present an approach to achieve these goals based on summarizing spatial relationships in the TME using spatial K functions, and then applying functional data analysis and random forest models to both predict outcomes of interest and identify important spatial relationships. This approach is shown to be effective in simulation experiments at both identifying important spatial interactions while also controlling the false discovery rate. We further used the proposed approach to interrogate two real data sets of Multiplexed Ion Beam Images of TMEs in triple negative breast cancer and lung cancer patients. The methods proposed are publicly available in a companion R package funkycells.

Abstract PO2-25-05: Spatial multiplexing of protein biomarkers for immune cell profiling of the tumor microenvironment with ChipCytometry

Abstract Understanding the spatial distribution of key immune cell populations is critical in advancing our understanding of cancer and the development of novel therapeutics. Historically, the spatial analysis of the tumor microenvironment (TME) has been limited to relatively low-plex immunohistochemical (IHC) or immunofluorescent (IF) assays, which were inadequate for deep immune cell profiling of the TME. Here, we present the analysis of fresh-frozen human breast tissue using spatial multiplexing technology called ChipCytometry, which combines iterative immuno-fluorescent staining using open-source antibodies for quantitative measure of virtually unlimited protein biomarkers on the same sample and high dynamic range imaging to facilitate quantitative phenotyping with single-cell resolution. In addition to traditional pathology review of the high-plex dataset, subsequent image analysis can be done using open-source or commercial software for advanced spatial analyses, including cluster analysis, neighborhood analysis and advanced data visualization. The results show precise expression levels for each of the protein biomarkers in the assay for each individual cell within the sample while maintaining spatial information about each cell. Dozens of immune cell subtypes were identified and quantified based on protein expression profiles. Spatial analysis of the samples revealed quantifiable heterogeneity of immune cell infiltration within the tumor samples, demonstrating the utility of the ChipCytometry platform for in-depth immune profiling in clinical samples. The ChipCytometry platform enables simultaneous detection of multiple protein biomarkers on a single tissue section for deep immune cell profiling in the TME. Combined with the single-cell spatial information, such datasets provide an opportunity for the discovery of new complex multiplexed biomarker signatures to inform therapeutic development and personalized medicine. Citation Format: Benton Berigan. Spatial multiplexing of protein biomarkers for immune cell profiling of the tumor microenvironment with ChipCytometry [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-25-05.

Acute Exposure to High-Altitude Results in Changes to Immune Cell Populations

High altitude is a challenging environment due to the reduced atmospheric pressure and oxygen availability, increased ultraviolet radiation, and reduced temperature relative to sea level. Previous studies in individuals who travel to high altitude demonstrate differential expression of genes involved in inflammation and innate immune system activation. This study aims to extend these findings by defining changes in immune cell population distributions and cell phenotypes during travel to high altitude. We hypothesized that acute high-altitude exposure would lead to shifts in immune cell populations toward a pro-inflammatory phenotype due to cellular stress caused by hypoxemia and tissue hypoxia. Participants (N=17) traveled to Barcroft Station in the White Mountain Research Center (3800 m). Whole blood was collected during fasting at sea level on the morning of ascent and each morning at high altitude for three days. Cells in whole blood were fixed and stained within 1-2 hours of collection and were processed via flow cytometry upon return to sea level. We observed a decrease in classical monocytes on the first (p=0.010) and second (p=0.003) mornings of high-altitude acclimatization to sea-level baseline, and an increase in intermediate monocytes on the first (p=0.013) and second (p=0.014) mornings at high altitude. We also observed an increase in B cells on the second (p=0.004) and third (p=0.004) mornings at high altitude compared to sea-level baseline (mean: 3.53%, SD: ±1.82). These results indicate that acute high altitude exposure results in a shift toward a pro-inflammatory monocyte phenotype and supports prior research suggesting a significant role of hypoxia in modulating B cell function. This research was supported through funding provided by a private donor. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Planar Cell Polarity Signaling: Coordinated Crosstalk for Cell Orientation.

The planar cell polarity (PCP) system is essential for positioning cells in 3D networks to establish the proper morphogenesis, structure, and function of organs during embryonic development. The PCP system uses inter- and intracellular feedback interactions between components of the core PCP, characterized by coordinated planar polarization and asymmetric distribution of cell populations inside the cells. PCP signaling connects the anterior-posterior to left-right embryonic plane polarity through the polarization of cilia in the Kupffer's vesicle/node in vertebrates. Experimental investigations on various genetic ablation-based models demonstrated the functions of PCP in planar polarization and associated genetic disorders. This review paper aims to provide a comprehensive overview of PCP signaling history, core components of the PCP signaling pathway, molecular mechanisms underlying PCP signaling, interactions with other signaling pathways, and the role of PCP in organ and embryonic development. Moreover, we will delve into the negative feedback regulation of PCP to maintain polarity, human genetic disorders associated with PCP defects, as well as challenges associated with PCP.

Abstract 5335: Immune cell population variations in the livers of commonly used mouse strains

Abstract Previous studies have shown that the distribution of major immune cell populations differ across mouse strains in peripheral blood and hematopoietic organs at baseline. Additionally, variations in immune responses exist between mouse strains in Leishmania spp. and Melanoma models, but these studies in the context of liver diseases including Non Alcoholic Fatty Liver Disease (NAFLD) and Hepatocellular Carcinoma (HCC) have not been carried out. With the effort to state if these variations exist within the liver, we performed comprehensive spectral flow cytometry analysis on the liver and spleens of three female mouse strains commonly used in cancer research (BALB/c, C57BL/6, and FVBN). NAFLD was induced by providing mice with a methionine choline deficient diet. To promote HCC, a single genotype (myc/p53+/-) was induced by administering transposon-based vectors to overexpress Myc-Luc and CRISPR/Cas-9 vectors to knock down p53 via hydrodynamic tail-vein injection. To confirm vector integration and monitor tumor growth (luciferase activity), in vivo imaging was performed at different time points. As a result, we confirm throughout this study that differences exist within immune cell populations of the liver and spleen at baseline. Moreover, we depict differences in the shift of immune cell populations across mouse strains in the pathologic states included. In NAFLD, there is an increase of dendritic cells (DCs), macrophages, NK cells, ILC1s, T regulatory cells (Tregs), TH1, and TH2, and a decrease of CD4+ T cells, B cells, γδ-T cells, and NKT cells in the liver across all mouse strains, when compared to controls. However, the population of neutrophils in BALB/c decreases, and the population of CD8+ T cells increases in C57BL/6 mice, which differs from the patterns of change seen in the other mouse strains. Moreover, in spleens, NAFLD promotes an increase of TH1 and NK cells, and a decrease of TH2 and NKT Cells across the mouse strains included in the study, whereas the patterns of change differ between mouse strains among the remaining immune cell types. When evaluating liver immune cell population shifts on our HCC model, BALB/c mice showed a decrease in macrophages and ILC1s, C57BL/6 mice showed a decrease in γδ-T cells, prominent shifts across Neutrophils, TH1, and NKT cells, and null changes in TH2 and CD4+ T cell shifts, and FVBN mice had a less prominent decrease of B cells, which differed from the shifts observed in the mouse strains used for comparison. Immune cell populations in the spleens of our HCC mouse model also presented with differences across the mouse strains studied. In conclusion, we highlight that key differences in immune profiles exist across commonly used mouse strains for cancer research in the presence of liver pathology including HCC, suggesting that mouse strains could be possible confounders in the study of immune oncology of HCC. Citation Format: Francisco J. Rodriguez-Matos, Patrick Huang, Rajiv Trehan, Benjamin Ruf, Chi Ma, Tim F. Greten. Immune cell population variations in the livers of commonly used mouse strains [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5335.

Abstract 5497: Towards a drag and drop spatial biology workflow: Introducing sample reinterrogation as a conduit for the progressive development and on-line analysis of high parameter spatial biology data

Abstract The potential for spatial biology in cancer research is understood and edified. With it we can understand the tumor microenvironment, unravel responsiveness to drug treatments and cell therapies, and ultimately stratify patients for targeted treatment and clinical trial enrollment. Yet, researchers exploring spatial biology may be discouraged by what can be a resource intensive exercise, and most importantly, a commitment of high value patient samples. Furthermore, the design of reagent panels used to study samples is not trivial, and a specimen’s unique biomarker expression profile may require adjustments. Here we present a novel solution that permits sample re-interrogation and in-flight adjustments of reagent panels in our spatial biology workflow. The CellScape™ platform for Precise Spatial Multiplexing paired with VistaPlex™ Assay Kits provide a ready-to-use cyclic multiplex immunofluorescence (IF) solution to interrogate fresh frozen and FFPE tissue samples. Tissues are mounted in enclosed fluidic chambers, while staining and imaging are conducted on the CellScape instrument. The experiment requires no additional autostainer equipment and is divided into separate staining and imaging rounds. The end user may therefore pause between rounds and conduct inter-round analyses, which can then guide decisions of whether and how to continue the experiment. To illustrate the benefit of this approach, we present a use case in which we applied VistaPlex antibody panels to reveal the spatial distribution of major immune cell populations. Inter-round analysis and conclusions were then drawn from this preliminary phenotype map before successive rounds of rationally planned staining were conducted to further deepen the depth and breadth of spatial phenotyping. The CellScape sample reinterrogation feature is a pragmatic spatial biology solution that optimizes the use of precious resources, whilst allowing researchers to generate informed decisions about antibody panel designs almost in real time. This enhanced utility may reduce the resistance to spatial biology among researchers working with samples that are limited or irreplaceable. Citation Format: Matthew H. Ingalls, Xenia Meshik, Charles E. Jackson, Kayla E. Cashion, Arne Christians, Anke Brix, Marcus Boettcher, J Spencer Schwarz, Oliver Braubach. Towards a drag and drop spatial biology workflow: Introducing sample reinterrogation as a conduit for the progressive development and on-line analysis of high parameter spatial biology data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5497.

Abstract 5389: Development of T-cell exclusion in melanoma

Abstract Immune checkpoint inhibitors (ICIs), which prevent immune cell exhaustion and boost an antitumor response, have shown remarkable treatment efficacy in patients with advanced melanoma. However, its efficacy is limited by the emergence of resistance associated with an immunosuppressive tumor microenvironment (TME). The contribution of abnormal tumor vasculature to limited immune cell infiltration into the tumor core has been reported but the mechanisms of its development are still elusive. We analyzed how tumor angiogenesis affects the immune cell exclusion at different time points of primary melanoma using syngeneic murine melanomas. The spatial distribution of various immune cell populations and vascular integrity were analyzed in whole tumor cross-sections via multiplex immunofluorescence staining. We found that the exclusion pattern of CD8+ T cells was less evident with a balanced distribution across the whole tumor regions at the early stage. However, as the tumor grows, there is a pronounced accumulation of CD8+ T cells at the tumor periphery with a conspicuous absence in the core. Tumor blood vessels were structurally uniform and functionally stable in the early developmental tumor but became unstable and leaky as the tumor progressed, which was associated with the development of CD8+ T-cell exclusion. To understand the mechanism underlying vascular regulation of immune exclusion during tumor progression, we will investigate the expression of genes related to tumor angiogenesis using spatial transcriptomic analysis and RNA sequencing of endothelial cells (CD45+CD31-) sorted from the murine melanomas. These results highlight the contribution of spatial tumor vascular destabilization to the T-cell exclusion development, implying the potential of targeting tumor vasculature to enhance immune activation and the therapeutic efficacy of ICI in melanoma. Citation Format: Ha-Ram Park, Hee Won Yang, Minah Kim. Development of T-cell exclusion in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5389.

Abstract 434: Understanding metabolic heterogeneity of estrogen receptor positive metastatic breast tumors using spatial transcriptomics and geographic information systems approaches

Abstract The tumor microenvironment consists of numerous cell populations showing diverse metabolic preferences, causing metabolic heterogeneity and therapy resistance. Fulvestrant, a clinically approved selective estrogen receptor (ER) degrader, is the standard of care for ER-positive breast cancer, yet resistance has been reported among metastatic breast cancer patients. In our previous studies, we showed such resistance is attributable to metabolic heterogeneity in the tumor microenvironment. Despite metabolic heterogeneity posing a common challenge in cancer research, current methods, such as histology and Magnetic Resonance Imaging, cannot explore nutrient uptake at transcript-level resolution with spatial context, making it difficult to understand the heterogeneity that affects cellular growth and metabolism. Visium Spatial Transcriptomics, a method that shows regional gene expression, is emerging as a powerful spatial analysis tool, and we integrated this method with geographic information systems to investigate the tumor microenvironment heterogeneity and highlight the importance of cell-microenvironment interactions. We developed a computational pipeline to visualize hotspots of spatially relevant genes using breast cancer metastatic samples from xenograft models and human patients. This pipeline integrates Visium tools and geospatial methods for processing transcriptome profiling data. We analyzed the degree of local spatial association based on Local Moran’s I to estimate regions with significant co-localization of single and multiple gene expressions within a tumor. We then leveraged the co-localized areas in the process of biomarker identification and revealing biological pathways. We also used unsupervised clustering of the complete transcriptome profiles to test the resemblance between identified clusters and hotspots as well as any disruption in the spatial structure of clusters in response to therapy or metastasis. Gene set enrichment analysis of these clusters revealed several glucose or lipid metabolism pathways, and mapping of the genes corresponding to each pathway showed mutually exclusive gene expression patterns in the sample. We also observed minimal co-localization of two metabolic pathways but extensive co-localization between metabolic genes and ER target genes, suggesting distinct metabolic preferences and spatial distributions of endocrine therapy resistant cell populations. Altogether, our analysis pipeline established a computational framework for characterizing the link between tumor microenvironment, local metabolism, and changes in transcriptional response to external stimuli. Our findings support the development of strategies to target different endocrine resistant regions using a combination of ER and metabolic signaling inhibitors. Citation Format: Jin Young Yoo, Sabrina Akter, Nandana Varma, Atharva Jain, Aiman Soliman, Zeynep Madak Erdogan. Understanding metabolic heterogeneity of estrogen receptor positive metastatic breast tumors using spatial transcriptomics and geographic information systems approaches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 434.

DOP87 Characterization of pathologic fibroblast and macrophage cell populations in colonic Crohn’s Disease with spatial transcriptomics

Abstract Background Single-cell transcriptomic data of the human intestine has shed new light on the cellular composition and heterogeneity present in healthy and diseased tissues. Nonetheless, little information is currently available on their spatial distribution within tissue structures and cellular neighborhoods, which is particularly relevant to infer the function of disease-specific cell types. Here, we apply spatial transcriptomics to healthy control (HC) and Crohn’s disease (CD) intestinal samples and provide a map of cell types across healthy and diseased colon. Methods Fresh frozen colonic sections from HC (n=1) and CD (n=3) patients were placed onto 10X Visium slides, which feature thousands of spatially barcoded spots, each capable of capturing RNA from 10-15 cells. To retrieve single-cell resolution, spots were deconvoluted according to the Cell2location approach using our previously generated human single cell RNA sequencing (scRNAseq) dataset1 as a reference. For validation and further analysis at single-cell resolution, a panel of 100 genes was measured using single molecule fluorescent in situ hybridization (Molecular Cartography) (Fig. 1A). Results Deconvolution analysis revealed the cellular composition of each spot across all four different tissue sections including epithelial, stromal and immune cell types. Here, we focused on studying the location and diversity of fibroblasts and macrophages given their plasticity during inflammation1,2. The most abundant fibroblast cell type in CD were the inflammation-associate (IAFs) and the GREM1+ subepithelial fibroblasts. These two subsets showed a distinct gene signature and location, suggesting different functions (Fig. 1B). Most GREM1+ fibroblasts co-expressed FGFR1 and were in proximity with endothelial cells (VWF+) expressing the VEGF receptor 2 KDR, highlighting a potential pro-angiogenic role of GREM1+ fibroblasts3 (Fig. 1C). Remarkably, GREM1 was abundantly expressed by CCL19+ fibroblastic reticular cells and TNC+ stromal cells, underlying the potential heterogeneity of GREM1+ fibroblasts. Regarding macrophages, we could identify an inflammation-specific population expressing PLA2G2D and PTGDS. These macrophages were mainly localized within granulomas surrounding M1 macrophages (Fig. 1D). While their function is unknown, their signature suggests they might be modulating inflammation through the production of anti-inflammatory lipid mediators4. Conclusion Using two different ST technologies, we resolved the tissue distribution of cell populations previously identified by scRNAseq and reveal their potential function based on their spatial location.

Role of bio-flavonols and their derivatives in improving mitochondrial dysfunctions associated with pancreatic tumorigenesis.

Mitochondria, a cellular metabolic center, efficiently fulfill cellular energy needs and regulate crucial metabolic processes, including cellular proliferation, differentiation, apoptosis, and generation of reactive oxygen species. Alteration in the mitochondrial functions leads to metabolic imbalances and altered extracellular matrix dynamics in the host, utilized by solid tumors like pancreatic cancer (PC) to get energy benefits for fast-growing cancer cells. PC is highly heterogeneous and remains unidentified for a longer time because of its complex pathophysiology, retroperitoneal position, and lack of efficient diagnostic approaches, which is the foremost reason for accounting for the seventh leading cause of cancer-related deaths worldwide. PC cells often respond poorly to current therapeutics because of dense stromal barriers in the pancreatic tumor microenvironment, which limit the drug delivery and distribution of antitumor immune cell populations. As an alternative approach, various natural compounds like flavonoids are reported to possess potent antioxidant and anticancerous properties and are less toxic than current chemotherapeutic drugs. Therefore, we aim to summarize the current state of knowledge regarding the pharmacological properties of flavonols in PC in this review from the perspective of mitigating mitochondrial dysfunctions associated with cancer cells. Our literature survey indicates that flavonols efficiently regulate cellular metabolism by scavenging reactive oxygen species, mitigating inflammation, and arresting the cell cycle to promote apoptosis in tumor cells via intrinsic mitochondrial pathways. In particular, flavonols proficiently inhibit the cancer-associated proliferation and inflammatory pathways such as EGFR/MAPK, PI3K/Akt, and nuclear factor κB in PC. Overall, this review provides in-depth evidence about the therapeutic potential of flavonols for future anticancer strategies against PC; still, more multidisciplinary human interventional studies are required to dissect their pharmacological effect accurately.

Innate lymphoid cell population distributions and related gene expression characteristics in blood from allergic and nonallergic patients with eosinophilic asthma

Innate lymphoid cell population distributions and related gene expression characteristics in blood from allergic and nonallergic patients with eosinophilic asthma

Modified Biejia Jianwan decoction restrains PD-L1-mediated immune evasion through the HIF-1α/STAT3/NF-κB signaling pathway

Ethnopharmacological relevanceModified Biejia Jianwan (M-BJJW), a Traditional Chinese Medicine (TCM) decoction, has exhibited great potential in treating hepatocellular carcinoma (HCC). However, its underlying functional mechanism still remains unknown. Aim of the studyThe study aimed to explore the anti-hepatocarcinogenic effects of M-BJJW, specifically its influence on PD-L1-mediated immune evasion in hypoxic conditions, and elucidate the related molecular mechanisms in HCC. Materials and methodsTo investigate the therapeutic efficacy and mechanisms underlying M-BJJW's effects on HCC, we employed a diethylnitrosamine (DEN)-induced rat model maintained for 120 days. Following model establishment, flow cytometry was utilized to assess the distribution of immune cell populations in peripheral blood, spleens, and tumor tissues after M-BJJW administration. Simultaneously, enzyme-linked immunosorbent assays (ELISA) were conducted to analyze cytokine profiles in serum samples. Immunohistochemistry was employed to determine the expression levels of crucial proteins within tumor tissues. Furthermore, HCC cells exposed to CoCl2 underwent Western blot analysis to validate the expression levels of HIF-1α, PD-L1, STAT3, and nuclear factor kappa B (NF-κB) p65. The modulatory effects of STAT3 and NF-κB p65 were investigated using specific inhibitors and activators in wild-type cell lines. High-performance liquid chromatography coupled with mass spectrometry (HPLC/MS) was utilized to identify the chemical constituents present in M-BJJW-medicated serum. The immunomodulatory properties and the anti-tumor activities of M-BJJW were evaluated by co-culturing with peripheral blood mononuclear cells (PBMC) and the CCK-8 assay. Additionally, we assessed M-BJJW's impact on hypoxia-induced alterations in HCC cell lines using immunofluorescence and Western blot assessments. ResultsM-BJJW exhibited substantial therapeutic advantages by effectively alleviating pathological deterioration within the HCC microenvironment. In the DEN-induced rat model, M-BJJW administration notably reduced tumor growth. Flow cytometry analyses revealed an increased proportion of Cytotoxic T lymphocytes (CTLs) accompanied by a simultaneous decrease in regulatory T cells (Tregs). ELISA data supported a marked decrease in pro-inflammatory cytokines, including interleukin-6 (IL-6), interleukin-10 (IL-10), and tumor necrosis factor α (TNF-α). Immunohistochemistry confirmed the suppressive effect of M-BJJW on the expression of HIF-1α and PD-L1. Notably, western blotting unveiled the role of HIF-1α in regulating PD-L1 expression via the STAT3 and NF-κB signaling pathways in HCC cell lines, which was validated using activators and inhibitors of STAT3 and NF-κB. The CCK-8 assay and co-culture techniques demonstrated the anti-tumor activity of M-BJJW. Immunofluorescence and western blotting further confirmed that M-BJJW-containing serum dose-dependently inhibited HIF-1α, PD-L1, p-STAT3, and p-p65 in hypoxic HCC cell lines. ConclusionsM-BJJW demonstrates significant therapeutic potential against HCC by influencing the hypoxic microenvironment, thereby regulating the immunosuppressive milieu. Specifically, M-BJJW modulates the HIF-1α/STAT3/NF-κB signaling pathway, leading to reduced PD-L1 expression and an elevated ratio of cytotoxic T lymphocytes (CTLs), while concurrently decreasing T regulatory cells (Tregs) and immunosuppressive factors. These synergistic effects aid in countering PD-L1-mediated immune evasion, presenting compelling pharmacological evidence supporting the clinical application of M-BJJW as a therapeutic approach for HCC.

Trichosanthin alleviates streptozotocin-induced type 1 diabetes mellitus in mice by regulating the balance between bone marrow-derived IL6+ and IL10+ MDSCs

Myeloid-derived suppressor cells (MDSCs) occupy a pivotal role in the intricate pathogenesis of the autoimmune disorder, Type 1 diabetes mellitus (T1DM). Since our previous work demonstrated that trichosanthin (TCS), an active compound of Chinese herb medicine Tian Hua Fen, regulated immune response, we aimed to clarify the efficacy and molecular mechanism of TCS in the treatment of T1DM. To this end, T1DM mouse model was established by streptozotocin (STZ) induction. The mice were randomly divided into normal control group (Ctl), T1DM group (STZ), TCS treated diabetic group (STZ + TCS) and insulin-treated diabetic group (STZ + insulin). Our comprehensive evaluation encompassed variables such as blood glucose, glycosylated hemoglobin, body weight, pertinent biochemical markers, pancreatic histopathology, and the distribution of immune cell populations. Furthermore, we meticulously isolated MDSCs from the bone marrow of T1DM mice, probing into the expressions of genes pertaining to the advanced glycation end product receptor (RAGE)/NF-κB signaling pathway through RT-qPCR. Evidently, TCS exhibited a substantial capacity to effectively counteract the T1DM-induced elevation in random blood glucose, glycosylated hemoglobin, and IL-6 levels in plasma. Pathological scrutiny underscored the ability of TCS to mitigate the damage incurred by islets. Intriguingly, TCS interventions engendered a reduction in the proportion of MDSCs within the bone marrow, particularly within the IL-6+ MDSC subset. In contrast, IL-10+ MDSCs exhibited an elevation following TCS treatment. Moreover, we observed a significant down-regulation of relative mRNA of pro-inflammatory genes, including arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), RAGE and NF-κB, within MDSCs due to the influence of TCS. It decreases total MDSCs and regulates the balance between IL-6+ and IL-10+ MDSCs thus alleviating the symptoms of T1DM. TCS also down-regulates the RAGE/NF-κB signaling pathway, making it a promising alternative therapeutic treatment for T1DM. Collectively, our study offered novel insights into the underlying mechanism by which TCS serves as a promising therapeutic intervention for T1DM.