Cell Subtypes Research Articles

KIR2DL5+CD8+ T cells associate with dietary lipid intake and are active in type 1 diabetes

BackgroundRecent studies have shown that KIR+CD8+ T cells play a role in suppressing autoimmunity by eliminating pathogenic CD4+ T cells. However, their specific role in type 1 diabetes (T1D) remains unclear. MethodsIn this study, we enrolled 108 patients diagnosed with T1D and 86 healthy individuals. We conducted flow cytometric analysis to examine the various subtypes of KIR+CD8+ T cells derived from peripheral blood mononuclear cells. Additionally, CD8+ T cells were isolated from the peripheral blood of T1D patients to assess the functions of different KIR+CD8+ T cell subtypes. To investigate the influence of lipids on the characteristics and activities of these T cell subtypes, the isolated CD8+ T cells were cultured with varying concentrations of palmitic acid (PA). Furthermore, we utilized an NSG (NOD scid gamma) mouse adoptive transfer model to assess the impact of dietary lipid intake on the functionality of KIR2DL5+CD8+ T cells in vivo. ResultsWe observed variations in circulating KIR+CD8+ T cell subtypes between patients with T1D and healthy controls. Notably, we observed a significant negative correlation between the frequencies of circulating KIR+CD8+ T cells and the titers of ZnT8 autoantibodies in individuals with T1D. Among these subtypes, KIR2DL5+CD8+ T cells demonstrated a positive association with dietary fat intake, characterized by increased perforin expression and reduced PD-1 expression. Importantly, KIR2DL5+CD8+ T cells exhibited enhanced proliferative capacity compared to other KIR+CD8+ T cell subsets. Palmitic acid (PA) was found to enhance the activation of KIR2DL5+CD8+ T cells and strengthened their ability to suppress CD4+ T cell proliferation in T1D patients. Moreover, dietary lipid intake significantly enhanced the functionality of KIR2DL5+CD8+ T cells in an NSG mouse adoptive transfer model. ConclusionOur findings suggest that lipid intake enhances the functionality of human KIR2DL5+CD8+ T cells and may offer implications for immunotherapy in T1D.

A novel method for cell deconvolution using DNA methylation in PCA space

BackgroundIn this study, we present a novel method for reference-based cell deconvolution using data from DNA methylation arrays. Different from existing methods like IDOL-Ext, which operate on probe-level data, our approach represents features in the principal component analysis (PCA) space for cell type deconvolution.ResultsOur method’s accuracy in estimating cell compositions is validated across various public datasets, including blood samples from glioma patients. It demonstrates precision comparable to IDOL-Ext, with R2 values ranging from 0.73 to 0.99 for most cell types, while offering improved discrimination between similar cell types, particularly T cell subtypes in glioma patient samples (R2 0.42–0.75 vs. 0.36–0.66 for IDOL-Ext). However, both methods showed lower accuracy for certain cell types, such as memory CD8 T cells in glioma patients (R2 0.42 vs. 0.36 for IDOL-Ext), highlighting the challenges in distinguishing closely related cell populations. We have made this method available as an R package “BloodCellDecon” on GitHub.ConclusionsOur study confirms the efficacy of cell type deconvolution in PCA space. The results indicate wide-ranging applicability and potential for adaptation to other forms of genomic data.

The Effect of Cuproptosis-Related Proteins on Macrophage Polarization in Mesothelioma is Revealed by scRNA-seq.

High invasiveness mesothelioma is a malignant tumor of the peritoneum or pleura. The effect of cuproptosis on mesothelioma (MESO) is still unknown, though. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets were used to identify differential genes linked to cuproptosis in mesothelioma. Multigene features were then created to assess the course of the disease. Use single-cell data and in vitro validation to uncover crucial gene regulation mechanisms. In MESO, we found nine differentially expressed genes linked to cuproptosis. Using univariate Cox and LASSO regression techniques, a 3-gene feature (P < 0.05) was created, showing a good predictive potential for survival time. According to the risk score, patients in the low-risk subset had a considerably greater survival rate than those in the high-risk subset (P = 0). The similar survival pattern and prediction performance are also seen in the validation queue. The findings of the drug sensitivity research indicate that in high-risk patients, vinblastine, paclitaxel, gefitinib, and erlotinib are sensitive medications (P < 0.05). Classical monocytes were identified as core cells connected to cuproptosis by the CellChat results. SLC31A1 is implicated in the positive regulation of M2 macrophage polarization, according to cell subtype analysis and in vitro confirmation. Genes linked to cuproptosis have a major influence on tumor immunity and can predict how MESO will progress.

Machine learning enabled classification of lung cancer cell lines co-cultured with fibroblasts with lightweight convolutional neural network for initial diagnosis

BackgroundIdentification of lung cancer subtypes is critical for successful treatment in patients, especially those in advanced stages. Many advanced and personal treatments require knowledge of specific mutations, as well as up- and down-regulations of genes, for effective targeting of the cancer cells. While many studies focus on individual cell structures and delve deeper into gene sequencing, the present study proposes a machine learning method for lung cancer classification based on low-magnification cancer outgrowth patterns in a 2D co-culture environment.MethodsUsing a magnetic well plate holder, circular pattern lung cancer cell clusters were generated among fibroblasts, and daily images were captured to monitor cancer outgrowth over a 9-day period. These outgrowth images were then augmented and used to train a convolutional neural network (CNN) model based on the lightweight TinyVGG architecture. The model was trained with pairs of classes representing three subtypes of NSCLC: A549 (adenocarcinoma), H520 (squamous cell carcinoma), and H460 (large cell carcinoma). The objective was to assess whether this lightweight machine learning model could accurately classify the three lung cancer cell lines at different stages of cancer outgrowth. Additionally, cancer outgrowth images of two patient-derived lung cancer cells, one with the KRAS oncogene and the other with the EGFR oncogene, were captured and classified using the CNN model. This demonstration aimed to investigate the translational potential of machine learning-enabled lung cancer classification.ResultsThe lightweight CNN model achieved over 93% classification accuracy at 1 day of outgrowth among A549, H460, and H520, and reached 100% classification accuracy at 7 days of outgrowth. Additionally, the model achieved 100% classification accuracy at 4 days for patient-derived lung cancer cells. Although these cells are classified as Adenocarcinoma, their outgrowth patterns vary depending on their oncogene expressions (KRAS or EGFR).ConclusionsThese results demonstrate that the lightweight CNN architecture, operating locally on a laptop without network or cloud connectivity, can effectively create a machine learning-enabled model capable of accurately classifying lung cancer cell subtypes, including those derived from patients, based upon their outgrowth patterns in the presence of surrounding fibroblasts. This advancement underscores the potential of machine learning to enhance early lung cancer subtyping, offering promising avenues for improving treatment outcomes in advanced stage-patients.

Multicellular 3D bioprinted human gallbladder carcinoma for in vitro mimicry of tumor microenvironment and intratumoral heterogeneity

Gallbladder carcinoma (GBC) is a malignant hepatobiliary cancer characterized by an intricate tumor microenvironments (TME) and heterogeneity. The traditional GBC 2D culture models cannot faithfully recapitulate the characteristics of the TME. Three-dimensional (3D) bioprinting enables the establishment of high-throughput and high-fidelity multicellular GBC models. In this study, we designed a concentric cylindrical tetra-culture model to reconstitute the spatial distribution of cells in tumor tissue, with the inner portion containing GBC cells, and the outer ring containing a mixture of endothelial cells, fibroblasts, and macrophages. We confirmed the survival, proliferation, biomarker expression and gene expression profiles of GBC 3D tetra-culture models. Hematoxylin-eosin (HE) and immunofluorescence staining verified the morphology and robust expression of GBC/endothelial/fibroblast/macrophage biomarkers in GBC 3D tetra-culture models. Single-cell RNA sequencing revealed two distinct subtypes of GBC cells within the model, glandular epithelial and squamous epithelial cells, suggesting the mimicry of intratumoral heterogeneity. Comparative transcriptome profile analysis among variousin vitromodels revealed that cellular interactions and the TME in 3D tetra-culture models reshaped the biological processes of tumor cells to a more aggressive phenotype. GBC 3D tetra-culture models restored the characteristics of the TME as well as intratumoral heterogeneity. Therefore, this model is expected to have future applications in tumor biology research and antitumor drug development.

Comparative profiling of whole-cell and exosome samples reveals protein signatures that stratify breast cancer subtypes

Identifying novel breast cancer biomarkers will improve patient stratification, enhance therapeutic outcomes, and help develop non-invasive diagnostics. We compared the proteomic profiles of whole-cell and exosomal samples of representative breast cancer cell subtypes to evaluate the potential of extracellular vesicles as non-invasive disease biomarkers in liquid biopsies. Overall, differentially-expressed proteins in whole-cell and exosome samples (which included markers for invasion, metastasis, angiogenesis, and drug resistance) effectively discriminated subtypes; furthermore, our results confirmed that the proteomic profile of exosomes reflects breast cancer cell-of-origin, which underscores their potential as disease biomarkers. Our study will contribute to identifying biomarkers that support breast cancer patient stratification and developing novel therapeutic strategies. We include an open, interactive web tool to explore the data as a molecular resource that can explain the role of these protein signatures in breast cancer classification.Graphical (A) We quantified proteomic profiles of breast cancer cells (BCCs) and breast cancer-derived exosomes (BCDEs) samples from four breast cancer cell lines representative of common breast cancer subtypes – Her2-positive (Her2, MDA-MB-453), Luminal A (LA, MCF7), Luminal B (LB, ZR-75), and triple-negative (TN, MDA-MB-231). (B) We independently performed four comparisons for BCCs and BCDEs, comparing each cell line against the remaining three. (C) We identified differentially-expressed proteins (DEPs) for BCCs and BCDEs, defined protein signatures, and functionally analyzed resulting networks. Through pathway inference analysis (PIA), we identified Kyoto Encyclopedia of genes and genomes (KEGG) subpaths and biological Gene Ontology (GO) terms that displayed differential activation. (D) We validated our proteomic signature using the Cancer Genome Atlas (TCGA) and the Cancer Proteome Atlas (TCPA) databases, verified that differentially-activated pathways in BCDEs caused a corresponding response in receptor cells, and confirmed that the BCDE proteomic signature reflects their cell-of-origin and identifies candidate disease biomarkers in liquid biopsies

Mll4 regulates tooth enamel development.

Amelogenesis, or enamel development, is a highly regulated process that leads to the formation of tooth enamel, which is critical for protecting teeth from decay and wear. Disruptions in the amelogenesis process can result in amelogenesis imperfecta, a group of genetic conditions characterized by inadequately formed enamel. This condition can include enamel hypoplasia, marked by thinning or underdevelopment of the enamel layer. Mutations in the MLL4 ( KMT2D ) gene, which encodes a histone H3-lysine 4-methyltransferase, are associated with Kabuki syndrome, a developmental disorder that can involve dental anomalies such as enamel hypoplasia. However, the specific role of MLL4 in amelogenesis and its underlying mechanisms remain poorly understood. To investigate the role of Mll4 in amelogenesis, we generated a conditional knockout mouse line with an ectoderm-specific deletion of Mll4 ( Krt14-Cre;Mll4 fl/fl , or Mll4 -cKO) and examined the gross, radiographic, histological, cellular, and molecular features in these mice. Micro-computed tomography and scanning electron microscopy analyses revealed that adult Mll4 -cKO mice exhibited 100% penetrant amelogenesis imperfecta, characterized by hypoplastic and hypomineralized enamel, partially phenocopying human Kabuki syndrome. Additionally, Mll4 -cKO neonates developed molar tooth germs with minor cusp shape alterations and mild delays in ameloblast differentiation at birth. RNA-seq analysis of the first molar tooth germ at birth revealed that approximately 33.7% of known amelogenesis-related genes were significantly downregulated in the Mll4 -cKO teeth. Intersection with Mll4 CUT&RUN-seq results identified 8 overlapping genes directly targeted by Mll4. Re-analysis of a single-cell RNA-seq dataset in the developing mouse incisor teeth revealed distinct roles for these genes in Mll4-regulated differentiation across various cell subtypes within the dental epithelium. Among these genes, Satb1 and Sp6 are likely directly targeted by Mll4 during the differentiation of pre-ameloblasts into ameloblasts. Taken together, we propose that Mll4 plays a crucial role in amelogenesis by directly activating key genes involved in ameloblast differentiation.

Relation of T Cell Profile with Vitamin D Receptor and Vitamin D-Binding Protein Gene Polymorphisms in Atopy.

Atopic diseases, including atopic dermatitis (AD) and allergic asthma (AA), are characterized by complex immune responses involving various T cells subsets and their cytokine profiles. It is assumed that single nucleotide polymorphisms (SNPs) in the Vitamin D receptor (VDR) gene and the Vitamin D-binding protein (GC) gene are related to the action of Vitamin D and, consequently, play a role in regulating the immune response. However, there is not enough data to unequivocally support the hypothesis about the relationship between T cells profile and VDR or GC SNPs. Two hundred sixty-six subjects (aged > 18 years) were involved in the study: 100 patients with mild or moderate AD, 85 patients with mild or moderate AA, and 81 healthy individuals. Blood cell counts were determined by standard methods. Flow cytometric analysis was used to evaluate CD4+ T-helper (Th) cell subtypes: Th2, Th1, Th17, and T regulatory (Treg) cells in peripheral blood. Measurements of cytokines, total immunoglobulin E (IgE), and Vitamin D levels in serum were evaluated by ELISA. Significantly higher levels of Th1, Th2, and Th17 cells, along with lower levels of Tregs, were found in patients with atopic diseases compared to healthy individuals. Additionally, higher serum levels of interleukin (IL) 5, IL-17A, and transforming growth factor-β1 (TGF-β1), as well as lower levels of IL-10, were observed in patients with atopic diseases than in control. The study established associations between VDR SNPs and immune profiles: the AA genotype of rs731236 was associated with increased Th2 and Th17 cells and a higher Th1/Th2 ratio; the GG genotype of rs731236 was linked to decreased serum IL-10 and TGF-β1 levels; and the TT genotype of rs11168293 was associated with increased IL-10 levels. Additionally, the GG genotype of GC gene SNP rs4588 was associated with reduced Th2 and Th17 lymphocytes, while the TT genotype of rs4588 was linked to decreased IL-10 levels. Furthermore, the CC genotype of rs7041 was associated with higher levels of Th2, Th17, IL-10, and IL-35, as well as reduced levels of TGF-β1, while the GG genotype of rs3733359 was associated with reduced IL-10 levels. In conclusion, our study demonstrates that the Vitamin D receptor gene single nucleotide polymorphisms rs731236 and rs11168293, along with polymorphisms in the Vitamin D-binding protein gene (rs4588, rs7041, rs3733359), are significantly associated with variations in T cell profiles in atopy. These variations may play a crucial role in promoting inflammation and provide insight into the genetic factors contributing to the pathogenesis of atopy.

Association of tumor-infiltrating lymphocytes with clinical outcomes in patients with triple-negative breast cancer receiving neoadjuvant chemotherapy: a systematic review and meta-analysis.

Triple-negative breast cancer (TNBC) presents a clinical challenge as an aggressive tumor, correlated with unfavorable prognosis. Tumor-infiltrating lymphocytes (TILs) have garnered interest as a potential prognostic biomarker. However, the disparity in outcomes between varying TILs rates remains inadequately explored. PubMed, Scopus, Web of Science, and Cochrane databases were searched for studies about the prognostic value of TILs in patients with TNBC receiving neoadjuvant chemotherapy. The hazard ratios (HRs) or odds ratios (ORs) were computed for binary endpoints, with 95% confidence intervals (CIs). Twenty-nine studies were included, involving a population of six thousand one hundred sixty-one (80.41%) with TNBC. The cut-off TILs value ranged from 10 to 60%, with 50% being the most related value. Compared with the low-TIL expression group, the disease-free survival (DFS) (HR 0.71; 95% CI 0.61-0.82; p < 0.00001) and overall survival (OS) (HR 0.76; 95% CI 0.63-0.90; p = 0.002) rates showed significant improvement with higher TIL infiltrations. In the subgroup analyses of the lymphocyte subtypes CD4 + and CD8 + , there was statistical significance favoring higher TILs rates in both subtypes, each associated with improved DFS (HR 0.48; 95% CI 0.33-0.71; p = 0.0002) and OS (HR 0.53; 95% CI 0.36-0.78; p = 0.001), regardless of which cell subtype was predominantly infiltrated. The complete pathological response analysis showed better rates for the higher TIL group than the control for both the TIL (OR 1.29; 95% CI 1.13-1.48; p = 0.0003) and Ki-67 (OR 2.74; 95% CI 2.01-3.73; p < 0.00001) analyses. Higher expressions of TILs in patients with TNBC were associated with improved significantly DFS, OS, and pCR outcomes.

Single-cell transcriptomics reveals writers of RNA modification-mediated immune microenvironment and cardiac resident Macro-MYL2 macrophages in heart failure

BackgroundHeart failure (HF), which is caused by cardiac overload and injury, is linked to significant mortality. Writers of RNA modification (WRMs) play a crucial role in the regulation of epigenetic processes involved in immune response and cardiovascular disease. However, the potential roles of these writers in the immunological milieu of HF remain unknown.MethodsWe comprehensively characterized the expressions of 28 WRMs using datasets GSE145154 and GSE141910 to map the cardiac immunological microenvironment in HF patients. Based on the expression of WRMs, the immunological cells in the datasets were scored.ResultsSingle-cell transcriptomics analysis (GSE145154) revealed immunological dysregulation in HF as well as differential expression of WRMs in immunological cells from HF and non-HF (NHF) samples. WRM-scored immunological cells were positively correlated with the immunological response, and the high WRM score group exhibited elevated immunological cell infiltration. WRMs are involved in the differentiation of T cells and myeloid cells. WRM scores of T cell and myeloid cell subtypes were significantly reduced in the HF group compared to the NHF group. We identified a myogenesis-related resident macrophage population in the heart, Macro-MYL2, that was characterized by an increased expression of cardiomyocyte structural genes (MYL2, TNNI3, TNNC1, TCAP, and TNNT2) and was regulated by TRMT10C. Based on the WRM expression pattern, the transcriptomics data (GSE141910) identified two distinct clusters of HF samples, each with distinct functional enrichments and immunological characteristics.ConclusionOur study demonstrated a significant relationship between the WRMs and immunological microenvironment in HF, as well as a novel resident macrophage population, Macro-MYL2, characterized by myogenesis. These results provide a novel perspective on the underlying mechanisms and therapeutic targets for HF. Further experiments are required to validate the regulation of WRMs and Macro-MYL2 macrophage subtype in the cardiac immunological milieu.

Comparison of ultrasound findings of papillary thyroid carcinoma subtypes based on the 2022 WHO classification of thyroid neoplasms.

The present study aimed to analyze and compare sonographic features of papillary thyroid carcinoma (PTC) subtypes to determine whether ultrasound (US) may aid in differentiating particular subtypes. This retrospective study enrolled 133 patients diagnosed with 142 histopathologically proven PTCs as per the fifth edition of the World Health Organization classification of thyroid neoplasms between January 2013 and May 2023. US features based on the American College of Radiology and European Thyroid Imaging and Reporting Data Systems (TIRADS), and histopathological characteristics of nodules were assessed and compared. Histopathological analysis yielded 55 (38.7%) classic PTC, 32 (22.5%) invasive encapsulated follicular variant (IEFV) PTC, 20 (14.1%) oncocytic subtype, 14 (9.9%) non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), 11 (7.8%) infiltrative follicular subtype, 7 (4.9%) tall cell subtype, 2 (1.4%) solid subtype, and 1 (0.7%) diffuse sclerosing subtype. The US findings indicating malignancy, such as taller-than-wide shape, irregular margins, echogenic foci, and higher TIRADS categories, were more frequently demonstrated in nodules with classic PTC and the tall cell subtype, in line with their histopathological features. Conversely, IEFV-PTC and NIFTP rarely exhibited these high-risk sonographic features. US appearance of the oncocytic subtype more frequently overlapped with IEFV-PTC, yet hypo/very hypoechoic nodules with larger nodular diameters and higher TIRADS scores may favor the diagnosis of this subtype. US features of certain subtypes may guide the differential diagnosis regarding shape, margin, echogenic foci, and TIRADS category of nodules; however, definitive subtyping is not yet possible using US images alone.

Primate-specific BTN3A2 protects against SARS-CoV-2 infection by interacting with and reducing ACE2

Coronavirus disease 2019 (COVID-19) is an immune-related disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The complete pathogenesis of the virus remains to be determined. Unraveling the molecular mechanisms governing SARS-CoV-2 interactions with host cells is crucial for the formulation of effective prophylactic measures and the advancement of COVID-19 therapeutics. We analyzed human lung single-cell RNA sequencing dataset to discern the association of butyrophilin subfamily 3 member A2 (BTN3A2) expression with COVID-19. The BTN3A2 gene edited cell lines and transgenic mice were infected by live SARS-CoV-2 in a biosafety level 3 (BSL-3) laboratory. Immunoprecipitation, flow cytometry, biolayer interferometry and competition ELISA assays were performed in BTN3A2 gene edited cells. We performed quantitative real-time PCR, histological and/or immunohistochemical analyses for tissue samples from mice with or without SARS-CoV-2 infection. The BTN3A2 mRNA level was correlated with COVID-19 severity. BTN3A2 expression was predominantly identified in epithelial cells, elevated in pathological epithelial cells from COVID-19 patients and co-occurred with ACE2 expression in the same lung cell subtypes. BTN3A2 targeted the early stage of the viral life cycle by inhibiting SARS-CoV-2 attachment through interactions with the receptor-binding domain (RBD) of the Spike protein and ACE2. BTN3A2 inhibited ACE2-mediated SARS-CoV-2 infection by reducing ACE2 invitro and invivo. These results reveal a key role of BTN3A2 in the fight against COVID-19. Identifying potential monoclonal antibodies which mimic BTN3A2 may facilitate disruption of SARS-CoV-2 infection, providing a therapeutic avenue for COVID-19. This study was supported by the National Natural Science Foundation of China (32070569, U1902215, and 32371017), the CAS "Light of West China" Program, and Yunnan Province (202305AH340006).

The single cell transcriptional landscape of fibrosarcoma.

235 Background: Fibrosarcoma (FS) is a relatively uncommon subtype of soft tissue sarcoma, which predominantly occurs in the extremities and girdles of elderly individuals. FS are famous for its high recurrence and metastasis rate. However, the current treatment regimens have shown poor efficacy in treating these progressive lesions. Therefore, a deep understanding of the tumor microenvironment characteristics of fibrosarcoma is needed to develop more effective drugs.Therefore, a deeper understanding of the tumor microenvironment characteristics of fibrosarcoma is needed for further development of therapeutic drugs. Methods: We performed single-cell transcriptome sequencing for the first time on 6 patients bearing with FS. Bulk-seq data of soft tissue sarcoma was downloaded from public database including TCGA and GEO for prognostic analysis. What' s more, a cohort of 54 FS patients was retrospectively collected for protein detection. Results: The tumor microenvironment landscape was characterized by the presence of malignant fibroblast, diverse macrophages, limited T-cell presence, and high levels of vascular infiltration. The expression of siglec15 was significantly upregulated in the malignant cells. And the prognostic significance of siglec15 was confirmed by the TCGA public database. What’s more, the high expression of siglec15 protein was negatively related to overall survival of fibrosarcoma patients from our institution. We also explored the interactions among different cell subtypes, especially the interactions between malignant cells and endothelial cells, as well as macrophages and endothelial cells, which not only promote tumor progression but also inhibit T-cell infiltration and function. Conclusions: In total, our work has uncovered the low T cell infiltration landscape of FS. The primary reason of insufficient immune infiltration may be due to the blockage of T cell extravasation caused by the interaction between endothelial cells, malignant cells and macrophages.

Investigation of the effect of macrophage and epithelial cell interaction in the progression of different subtypes of breast cancer.

10 Background: In the realm of tumor progression, the immunosuppressive role of macrophages has been well-established. However, a significant lacuna persists concerning the mechanisms through which epithelial cells regulate macrophages. Furthermore, the precise manner in which macrophages modulate breast cancer cells remains unclear. Hence, the primary objective of the current investigation is to delve into the influence of macrophages on the progression of distinct subtypes of breast cancer. Methods: Human monocyte cell-derived macrophages (M0) were cultivated in the presence of conditioned media (CM) from various subtypes of breast cancer cells. Conversely, human luminal breast cancer cell line T47D, and basal cell line MDA MB 231 were cultured in the presence of CM from macrophages. Results: When macrophages were incubated with CM of T47D, they exhibited a spindle-shaped morphology with pseudopodia. Conversely, exposure to CM of MDA MB 231 induced macrophages to adopt a foamy, round shape with numerous filopodia. Flow cytometry analysis revealed that T47D-CM promoted a higher proportion of CD80+ cells, while MDA MB 231-CM led to an increase in both CD206+ and CD80+ cells. Moreover, both T47D and MDA MB 231-CM escalated the production of various cytokines including IL-1β, IL-2, IL-4, IL-5, IL-7, IL-12(p70), IL-13, IL-17, G-CSF, IFN-γ, and MIP-1β. Intriguingly, MDA MB 231-CM induced a significant increase in IL-6, GM-CSF, and TNF-α. Subsequent cultivation of cancer cells in the presence of macrophage-CM resulted in a marked proliferation of MDA MB 231 cells, while T47D cell proliferation decreased significantly. Correspondingly, there was a notable increase in apoptosis among T47D cells. Scratch wound healing assays revealed heightened migration of MDA MB 231 cells following treatment with macrophage-CM, whereas there was negligible alteration in T47D cell migration. Proteomic analysis unveiled dysregulation of 247 and 596 proteins in MDA MB 231 and T47D cells, respectively. Particularly noteworthy were three proteins—MDHM, H1.5, and LEG8—abundant in MDA MB 231 cells, yet scarce in T47D cells. These proteins have been implicated in promoting tumor growth across various cancer types. Conclusions: This study first time elucidates subtype specific role of macrophage in breast tumour. In triple-negative breast cancer, infiltrating macrophages induce an immunosuppressive effect, altering cytokine expression and fostering the expression of tumor-promoting factors in epithelial cells, thereby facilitating cellular proliferation and metastasis. Conversely, in luminal breast cancer, infiltrating macrophages exhibit a predominantly pro-inflammatory profile, resulting in minimal tumor-promoting effects. Key Words: Breast Cancer, Macrophage polarization, Conditioned Media, Cytokines, Proteomics. Acknowledgements, DBT – Govt of India, NIBMG, Kalyani.

Optics-free Spatial Genomics for Mapping Mouse Brain Aging.

Spatial transcriptomics has revolutionized our understanding of cellular network dynamics in aging and disease by enabling the mapping of molecular and cellular organization across various anatomical locations. Despite these advances, current methods face significant challenges in throughput and cost, limiting their utility for comprehensive studies. To address these limitations, we introduce IRISeq (Imaging Reconstruction using Indexed Sequencing), a optics-free spatial transcriptomics platform that eliminates the need for predefined capture arrays or extensive imaging, allowing for the rapid and cost-effective processing of multiple tissue sections simultaneously. Its capacity to reconstruct images based solely on sequencing local DNA interactions allows for profiling of tissues without size constraints and across varied resolutions. Applying IRISeq, we examined gene expression and cellular dynamics in thirty brain regions of both adult and aged mice, uncovering region-specific changes in gene expression associated with aging. Further cell type-centric analysis further identified age-related cell subtypes and intricate changes in cell interactions that are distinct to certain spatial niches, emphasizing the unique aspects of aging in different brain regions. The affordability and simplicity of IRISeq position it as a versatile tool for mapping region-specific gene expression and cellular interactions across various biological systems.

Peptide hydrogel based electrochemical biosensor for simultaneous monitoring ofH2O2 and NO released from three-dimensional cultured breast cancer cells.

Anantifouling peptide hydrogel-based electrochemical biosensor was developedfor real-time monitoring of hydrogen peroxide (H2O2) and nitric oxide (NO) released by 3D cultured breast cancer cells upon drug stimulation. Platinum nanoparticles (Pt NPs) were electrodeposited on titanium mesh (Pt NPs/TM) to enhance sensitivity and shown topossess excellent electrocatalytic ability toward H2O2 and NO. The composite hydrogel formed by co-assembling of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF) and a fluorine methoxycarbonyl group-functionalized Lys-(Fmoc)-Asp was coated on Pt NPs/TM electrode surface to provide cellular scaffolding. Their favorable biocompatibility promoted cell adhesion and growth, while good hydrophilicity endowed the sensor with greatly enhanced antifouling capability in complex cell culture environments. The biosensor successfully determined H2O2 and NO secretion from both non-metastatic and metastatic breast cancer cells in real time. Our results demonstrated robust associations between reactive oxygen species (ROS) and reactive nitrogen species (RNS) production and cell malignancy, with the main difference in oxidative stress between the two subtypes of cells being NO release, particularly emphasizing RNS's critical leading in driving cancer metastasis and invasion progression. This sensor holds great potential for cell-release research under the in vivo-like microenvironment and could reveal RNS as an attractive therapeutic target for treating breast cancer.

Deciphering single-cell transcriptomic landscape of tumors in colorectal cancer treated with photothermal semiconducting polymers to design the combination therapy with checkpoint blockades for inhibition of tumor progression and metastasis

Immunotherapy is often less effective for tumors with “immune-excluded,” or “immune-desert” microenvironment. To circumvent this hurdle, new therapeutic strategies need to be designed to reprogram the tumor microenvironment (TME). It is well known that photothermal therapy (PTT) can prime the TME and provoke the systemic anti-tumor immunity. But few studies perform extensive exploration in depth to decipher the changes in TME after PTT with cutting-edge technology besides conventional flow cytometry analysis. In this study, we designed a nanosystem consisting of organic semiconductor polymer liposome nanoparticles (Y8 NPs) as a multimodal imaging and photothermal agent to image and treat tumors. Upon laser irradiation, Y8 NPs in tumors could rapidly increase the temperature, induce massive cancer cell apoptosis and also promote the immunogenic cell death (ICD), ultimately remodulating the TME. We employed single cell RNA sequencing (scRNA-seq) technology to comprehensively explore transcriptomic profiling of individual cells constituting TME, demonstrating heterogenous alterations in the subtypes of immune cells, even tumor cells. Considering the findings by scRNA-seq and TME remodulation, the combinational strategy with checkpoint blockade PD-1 antibody was designed to treat the tumors, demonstrating that the combination not only impedes primary tumor progression but also produce profound abscopal anti-tumor effect. In conclusion, we provide a simple strategy for the remodulation of TME with a photothermal nanosystem to achieve activation of anti-tumor immunity, and suppress primary and metastatic tumor progression.

OXidative Stress PREDictor: A Supervised Learning Approach for Annotating Cellular Oxidative Stress States in Inflammatory Cells

Oxidative stress, characterized by an imbalance between reactive oxygen species (ROS) and antioxidants, plays a pivotal role in inflammatory responses associated with both chronic diseases and acute injuries. In this study, OXidative Stress PREDictor (OxSpred), a supervised learning model tailored to accurately annotate the oxidative stress state of innate immune cells at the single‐cell level, is introduced. Compared to the traditional gene‐set‐variation‐analysis‐based enrichment method, OxSpred demonstrates superior accuracy with an area under the receiver operating characteristic curve of 0.89 and offers interpretable embeddings with significant biological relevance. Using the predicted ROS states, precise elucidation and interpretation of the roles of novel innate immune cell subtypes can be achieved. Overall, OxSpred enhances the utility of single‐cell transcriptomic datasets by providing a robust in silico method for determining intracellular oxidative stress states, thereby enriching the understanding of innate immune cell functions during inflammation.

Abstract Mo126: A sex-specific CD4 + T cell response limits Coxsackievirus B pathogenesis in mice.

Coxsackievirus B3 (CVB3) is an enteric virus that is a primary cause of inflammation of the heart muscle, known as viral myocarditis. Viral myocarditis is a significant cause of heart failure, and nearly 40,000 cases are reported each year. Unfortunately, approximately 5% of CVB3 infections are fatal. Unfortunately, no vaccines or drugs are available for this virus. Interestingly, there is a sex bias in viral myocarditis where men are more susceptible than women. Unfortunately, the underlying basis for the sex bias in infection is incompletely understood. We recently determined that T cells play an essential role in CVB3 clearance using a novel oral inoculation mouse model. Here, we show a sex difference in the CD4 + T cell response to CVB3 that is important in limiting viral pathogenesis. We found that CVB3 induced CD4 + cell expansion in female mice but not in male mice. CVB3 infection also led to the expansion of CD62L lo CD4 + T cells in the mesenteric lymph node and spleen of female but not male mice as early as five days post-inoculation, indicative of activation. Using a recombinant CVB3 virus expressing a model CD4 + T cell epitope, we found that the expansion of CD4 + T cells in females is viral-specific and not due to bystander activation. Finally, the depletion of CD4 + T cells before infection led to enhanced mortality, indicating that CD4 + T cells protect against CVB3 in female mice. We are also currently investigating the impact of CD4 + T cell subtypes, and the role of intestinal T cells play in limiting intestinal CVB3 replication and dissemination. These data demonstrate that CVB3 induces a CD4 + T cell response in female mice and highlight the importance of sex-specific immune responses to viral pathogens.

Spatial profiling of non-small cell lung cancer provides insights into tumorigenesis and immunotherapy response

Lung cancer is the second most common cancer worldwide and a leading cause of cancer-related deaths. Despite advances in targeted therapy and immunotherapy, the prognosis remains unfavorable, especially in metastatic cases. This study aims to identify molecular changes in non-small cell lung cancer (NSCLC) patients based on their response to treatment. Using tumor and matched immune cell rich peritumoral tissues, we perform a retrospective, comprehensive spatial transcriptomic analysis of a proven malignant NSCLC sample treated with immune checkpoint inhibitor (ICI). In addition to T cells, other immune cell types, such as B cells and macrophages, were also activated in responders to ICI treatment. In particular, B cells and B cell-mediated immunity pathways are consistently found to be activated. Analysis of the histologic subgroup (lung squamous cell carcinoma, LUSC; lung adenocarcinoma, LUAD) of NSCLC also confirms activation of B cell mediated immunity. Analysis of B cell subtypes shows that B cell subtypes were more activated in immune cell-rich tissues near tumor tissue. Furthermore, increased expression of B cell immunity-related genes is associated with better prognosis. These findings provide insight into predicting ICI treatment responses and identifying appropriate candidates for immunotherapy in NSCLC patients.