Complement C1q (C1qA, C1qB, and C1qC) May Be a Potential Prognostic Factor and an Index of Tumor Microenvironment Remodeling in Osteosarcoma

Novel tumor-associated macrophage populations and subpopulations by single cell RNA sequencing

Tumor-associated macrophages (TAMs) are present in almost all solid tumor tissues. 16They play critical roles in immune regulation, tumor angiogenesis, tumor stem cell activation, tumor invasion and metastasis, and resistance to therapy. However, it is unclear how TAMs perform these functions. With the application of single-cell RNA sequencing (scRNA-seq), it has become possible to identify TAM subpopulations associated with distinct functions. In this review, we discuss four novel TAM subpopulations in distinct solid tumors based on core gene signatures by scRNA-seq, including FCN1 +, SPP1 +, C1Q + and CCL18 + TAMs. Functional enrichment and gene expression in scRNA-seq data from different solid tumor tissues found that FCN1 + TAMs may induce inflammation; SPP1 + TAMs are potentially involved in metastasis, angiogenesis, and cancer cell stem cell activation, whereas C1Q + TAMs participate in immune regulation and suppression; And CCL18 + cells are terminal immunosuppressive macrophages that not only have a stronger immunosuppressive function but also enhance tumor metastasis. SPP1 + and C1Q + TAM subpopulations can be further divided into distinct populations with different functions. Meanwhile, we will also present emerging evidence highlighting the separating macrophage subpopulations associated with distinct functions. However, there exist the potential disconnects between cell types and subpopulations identified by scRNA-seq and their actual function.

Reanalysis and validation of the transcriptional pleural fluid signature in pleural tuberculosis

Introduction

Pleural tuberculosis (PlTB), the most common site of extrapulmonary TB, is characterized by a paucibacillary nature and a compartmentalized inflammatory response in the pleural cavity, both of which make diagnosis and management extremely challenging. Although transcriptional signatures for pulmonary TB have already been described, data obtained by using this approach for extrapulmonary tuberculosis and, specifically, for pleural tuberculosis are scarce and heterogeneous. In the present study, a set of candidate genes previously described in pulmonary TB was evaluated to identify and validate a transcriptional signature in clinical samples from a Brazilian cohort of PlTB patients and those with other exudative causes of pleural effusion.

Methods

As a first step, target genes were selected by a random forest algorithm with recursive feature elimination (RFE) from public microarray datasets. Then, peripheral blood (PB) and pleural fluid (PF) samples from recruited patients presenting exudative pleural effusion were collected during the thoracentesis procedure. Transcriptional analysis of the selected top 10 genes was performed by quantitative RT-PCR (RT-qPCR).

Results

Reanalysis of the public datasets identified a set of candidate genes (CARD17, BHLHE40, FCGR1A, BATF2, STAT1, BTN3A1, ANKRD22, C1QB, GBP2, and SEPTIN4) that demonstrated a global accuracy of 89.5% in discriminating pulmonary TB cases from other respiratory diseases. Our validation cohort consisted of PlTB (n = 35) patients and non-TB (n = 34) ones. The gene expressions of CARD17, GBP2, and C1QB in PF at diagnosis were significantly different between the two (PlTB and non-TB) groups (p < 0.0001). It was observed that the gene expressions of CARD17 and GBP2 were higher in PlTB PF than in non-TB patients. C1QB showed the opposite behavior, being higher in the non-TB PF. After anti-TB therapy, however, GBP2 gene expression was significantly reduced in PlTB patients (p < 0.001). Finally, the accuracy of the three above-cited highlighted genes in the PF was analyzed, showing AUCs of 91%, 90%, and 85%, respectively. GBP2 was above 80% (sensitivity = 0.89/specificity = 0.81), and CARD17 showed significant specificity (Se = 0.69/Sp = 0.95) in its capacity to discriminate the groups.

Conclusion

CARD17, GBP2, and C1QB showed promise in discriminating PlTB from other causes of exudative pleural effusion by providing accurate diagnoses, thus accelerating the initiation of anti-TB therapy.

Comprehensive Analysis Reveals Prognostic and Therapeutic Immunity-Related Biomarkers for Pediatric Metastatic Osteosarcoma

Background and Objectives: Osteosarcoma, the most prevalent malignant bone tumor in children and adolescents, presents a complex pathogenesis characterized by various genetic and epigenetic alterations. This study aims to identify key differentially expressed genes (DEGs) in pediatric osteosarcoma, with a focus on those influencing metastasis and patient survival. Materials and Methods: We utilized the GSE33382 dataset from the GEO database for a comprehensive bioinformatic analysis. This included a protein-protein interaction (PPI) network analysis, Cox regression, and Kaplan-Meier survival analysis to identify central DEGs associated with osteosarcoma metastasis and patient survival. Results: Our analysis identified 88 DEGs related to osteosarcoma metastasis. Among them, three survival-related central DEGs-C1QA, CD74, and HLA-DMA-were significantly linked to patient outcomes. Further correlation analysis established a strong relationship between these genes, tumor mutation burden (TMB), immune checkpoint gene expression, and overall survival. Notably, C1QA and CD74 exhibited higher expression in non-metastatic osteosarcoma cases, suggesting a potential role in disease progression. Conclusions: The identified DEGs, particularly C1QA, CD74, and HLA-DMA, may serve as critical biomarkers for pediatric osteosarcoma prognosis and potential targets for immunotherapy. These findings provide a deeper understanding of the molecular landscape of osteosarcoma and open new avenues for therapeutic intervention.

C-C Motif Chemokine Ligand 5 (CCL5): A Potential Biomarker and Immunotherapy Target for Osteosarcoma

BACKGROUND

Osteosarcoma (OS) is the most common primary malignant tumor of bone tissue, which has an insidious onset and is difficult to detect early, and few early diagnostic markers with high specificity and sensitivity. Therefore, this study aims to identify potential biomarkers that can help diagnose OS in its early stages and improve the prognosis of patients.

METHODS

The data sets of GSE12789, GSE28424, GSE33382 and GSE36001 were combined and normalized to identify Differentially Expressed Genes (DEGs). The data were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) and Disease Ontology (DO). The hub gene was selected based on the common DEG that was obtained by applying two regression methods: the Least Absolute Shrinkage and Selection Operator (LASSO) and Support vVector Machine (SVM). Then the diagnostic value of the hub gene was evaluated in the GSE42572 data set. Finally, the correlation between immunocyte infiltration and key genes was analyzed by CIBERSORT.

RESULTS

The regression analysis results of LASSO and SVM are the following three DEGs: FK501 binding protein 51 (FKBP5), C-C motif chemokine ligand 5 (CCL5), complement component 1 Q subcomponent B chain (C1QB). We evaluated the diagnostic performance of three biomarkers (FKBP5, CCL5 and C1QB) for osteosarcoma using receiver operating characteristic (ROC) analysis. In the training group, the area under the curve (AUC) of FKBP5, CCL5 and C1QB was 0.907, 0.874 and 0.676, respectively. In the validation group, the AUC of FKBP5, CCL5 and C1QB was 0.618, 0.932 and 0.895, respectively. It is noteworthy that these genes were more expressed in tumor tissues than in normal tissues by various immune cell types, such as plasma cells, CD8+ T cells, T regulatory cells (Tregs), activated NK cells, activated dendritic cells and activated mast cells. These immune cell types are also associated with the expression levels of the three diagnostic genes that we identified.

CONCLUSION

We found that CCL5 can be considered an early diagnostic gene of osteosarcoma, and CCL5 interacts with immune cells to influence tumor occurrence and development. These findings have important implications for the early detection of osteosarcoma and the identification of novel therapeutic targets.

An integrative analysis of single-cell and bulk transcriptome and bidirectional mendelian randomization analysis identified C1Q as a novel stimulated risk gene for Atherosclerosis

Background

The role of complement component 1q (C1Q) related genes on human atherosclerotic plaques (HAP) is less known. Our aim is to establish C1Q associated hub genes using single-cell RNA sequencing (scRNA-seq) and bulk RNA analysis to diagnose and predict HAP patients more effectively and investigate the association between C1Q and HAP (ischemic stroke) using bidirectional Mendelian randomization (MR) analysis.

Methods

HAP scRNA-seq and bulk-RNA data were download from the Gene Expression Omnibus (GEO) database. The C1Q-related hub genes was screened using the GBM, LASSO and XGBoost algorithms. We built machine learning models to diagnose and distinguish between types of atherosclerosis using generalized linear models and receiver operating characteristics (ROC) analyses. Further, we scored the HALLMARK_COMPLEMENT signaling pathway using ssGSEA and confirmed hub gene expression through qRT-PCR in RAW264.7 macrophages and apoE-/- mice. Furthermore, the risk association between C1Q and HAP was assessed through bidirectional MR analysis, with C1Q as exposure and ischemic stroke (IS, large artery atherosclerosis) as outcomes. Inverse variance weighting (IVW) was used as the main method.

Results

We utilized scRNA-seq dataset (GSE159677) to identify 24 cell clusters and 12 cell types, and revealed seven C1Q associated DEGs in both the scRNA-seq and GEO datasets. We then used GBM, LASSO and XGBoost to select C1QA and C1QC from the seven DEGs. Our findings indicated that both training and validation cohorts had satisfactory diagnostic accuracy for identifying patients with HPAs. Additionally, we confirmed SPI1 as a potential TF responsible for regulating the two hub genes in HAP. Our analysis further revealed that the HALLMARK_COMPLEMENT signaling pathway was correlated and activated with C1QA and C1QC. We confirmed high expression levels of C1QA, C1QC and SPI1 in ox-LDL-treated RAW264.7 macrophages and apoE-/- mice using qPCR. The results of MR indicated that there was a positive association between the genetic risk of C1Q and IS, as evidenced by an odds ratio (OR) of 1.118 (95%CI: 1.013-1.234, P = 0.027).

Conclusion

The authors have effectively developed and validated a novel diagnostic signature comprising two genes for HAP, while MR analysis has provided evidence supporting a favorable association of C1Q on IS.

Research trends and hotspots in the immune microenvironment related to osteosarcoma and tumor cell aging: a bibliometric and visualization study

Background

It is well known that cancers have a common feature that even if the environment is extremely poor in nutrients, they can still make good use of them to maintain viability as well as to produce new biomass, which is one of the reasons why tumor cells are powerfully less susceptible to senescence and death. The microenvironment has a profound impact on the senescence as well as the growth and development of tumor cells, and it is also the focus of scientists' research because it may even affect the discovery of the treatment and pathogenesis of cancer. And so the study of the microenvironment in the tumor cells is of great significance to the analysis of the tumor cells as well as to the impact of their senescence. Similarly, the microenvironment of osteosarcoma is also crucial for its impact, but to our knowledge, there is no bibliometric study that systematically analyzes and describes the trends and future hotspots in this field of research as we do, and we are going to fill this gap in this study.

Methods

We searched the Web Science Core Collection 2010-2023 in WOS on August 1, 2023. Based on the criteria needed for the search, we retained articles that matched the topic, excluded studies other than articles and reviews, and selected only studies whose language was English. We performed an intuitive visualization and bibliometric approach to analyze the research content in this field and a systematic visualization of global trends and hotspots in the research of osteosarcoma and the microenvironment, for which we used multiple specialized For this purpose, we used several specialized software packages, such as VOSviewer and the Bibliometrix package for R software. Because research in this area of osteosarcoma and the microenvironment has begun to gain popularity in the last 10 years or so, and is a very novel piece of research, there were almost no studies in this area prior to 2010 and they were not very informative, and in the end, we chose to look at studies from after 2010.

Results

Based on the criteria needed for the search, resulting in a final selection of 821 articles. In the research area related to osteosarcoma and microenvironment, we found that China in Asia and the United States in North America and Italy in Europe were the three countries or regions with the highest number of published articles. In addition, the institution that published the most research in this area was Shanghai Jiao Tong University. In terms of publications in the field of osteosarcoma and microenvironmental research, Baldini, Heymann, and Avnet are among the top 3 authors. The terms "cancer", "cells" and "expression" are found to be more commonly employed.

Conclusion

Using a variety of highly specialized software, we have undertaken a visual and bibliometric study of the current state of research and potential future hotspots in the field of osteosarcoma and microenvironment research. The microenvironment has a profound impact on the senescence and growth and development of cells in tumors, including osteosarcoma, and may even influence the discovery of cancer treatment and pathogenesis, and is also a hotspot and focus that scientists have begun to gradually study in recent years. This analysis and visualization will help guide future research in the field.

METTL3-mediated m6A methylation of C1qA regulates the Rituximab resistance of diffuse large B-cell lymphoma cells

Rituximab has been incorporated into the standard treatment regimen for diffuse large B-cell lymphoma (DLBCL), and induces the death of tumor cells via complement-dependent cytotoxicity (CDC). Unfortunately, the resistance of DLBCL cells to Rituximab limits its clinical usefulness. It remains unclear whether the complement system is related to Rituximab resistance in DLBCL. A Rituximab-resistant DLBCL cell line (Farage/R) was generated under the stress of Rituximab. Constituent proteins of the complement system in wild-type Farage cells (Farage/S) and Farage/R cells were analyzed by qPCR, western blotting, and immunofluorescence. In vitro and in vivo knockdown and overexpression studies confirmed that the complement 1Q subcomponent A chain (C1qA) was a regulator of Rituximab resistance. Finally, the mechanism by which C1qA is regulated by m6A methylation was explored. The reader and writer were identified by pull-down studies and RIP-qPCR. Activity of the complement system in Farage/R cells was suppressed. C1qA expression was reduced in Farage/R cells due to post-transcriptional regulation. Furthermore, in vitro and in vivo results showed that C1qA knockdown in Farage/S cells decreased their sensitivity to Rituximab, and C1qA overexpression in Farage/R cells attenuated the Rituximab resistance of those cells. Moreover, METTL3 and YTHDF2 were proven to be the reader and writer for m6A methylation of C1qA, respectively. Knockdown of METTL3 or YTHDF2 in Farage/R cells up-regulated C1qA expression and reduced their resistance to Rituximab. In summary, the aberrant downregulation of C1qA was related to Rituximab resistance in DLBCL cells, and C1qA was found to be regulated by METTL3- and YTHDF2-mediated m6A methylation. Enhancing the response of the complement system via regulation of C1qA might be an effective strategy for inhibiting Rituximab resistance in DLBCL.

Extracellular Vesicles as Possible Plasma Markers and Mediators in Patients with Sepsis-Associated Delirium-A Pilot Study

Patients with sepsis-associated delirium (SAD) show severe neurological impairment, often require an intensive care unit (ICU) stay and have a high risk of mortality. Hence, useful biomarkers for early detection of SAD are urgently needed. Extracellular vesicles (EVs) and their cargo are known to maintain normal physiology but also have been linked to numerous disease states. Here, we sought to identify differentially expressed proteins in plasma EVs from SAD patients as potential biomarkers for SAD. Plasma EVs from 11 SAD patients and 11 age-matched septic patients without delirium (non-SAD) were isolated by differential centrifugation, characterized by nanoparticle tracking analysis, transmission electron microscopy and Western blot analysis. Differential EV protein expression was determined by mass spectrometry and the resulting proteomes were characterized by Gene Ontology term and between-group statistics. As preliminary results because of the small group size, five distinct proteins showed significantly different expression pattern between SAD and non-SAD patients (p ≤ 0.05). In SAD patients, upregulated proteins included paraoxonase-1 (PON1), thrombospondin 1 (THBS1), and full fibrinogen gamma chain (FGG), whereas downregulated proteins comprised immunoglobulin (IgHV3) and complement subcomponent (C1QC). Thus, plasma EVs of SAD patients show significant changes in the expression of distinct proteins involved in immune system regulation and blood coagulation as well as in lipid metabolism in this pilot study. They might be a potential indicator for to the pathogenesis of SAD and thus warrant further examination as potential biomarkers, but further research is needed to expand on these findings in longitudinal study designs with larger samples and comprehensive polymodal data collection.

An in vitro model of human hematopoiesis identifies a regulatory role for the aryl hydrocarbon receptor

In vitro models to study simultaneous development of different human immune cells and hematopoietic lineages are lacking. We identified and characterized, using single-cell methods, an in vitro stromal cell-free culture system of human hematopoietic stem and progenitor cell (HSPC) differentiation that allows concurrent development of multiple immune cell lineages. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor influencing many biological processes in diverse cell types. Using this in vitro model, we found that AHR activation by the highly specific AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin, drives differentiation of human umbilical cord blood-derived CD34+ HSPCs toward monocytes and granulocytes with a significant decrease in lymphoid and megakaryocyte lineage specification that may lead to reduced immune competence. To our knowledge, we also discovered for the first time, using single-cell modalities, that AHR activation decreased the expression of BCL11A and IRF8 in progenitor cells, which are critical genes involved in hematopoietic lineage specification processes at both transcriptomic and protein levels. Our in vitro model of hematopoiesis, coupled with single-cell tools, therefore allows for a better understanding of the role played by AHR in modulating hematopoietic differentiation.

Single-Cell RNA Sequencing Analysis of the Early Postnatal Mouse Lens Epithelium

Purpose

The lens epithelium maintains the overall health of the organ. We used single-cell RNA sequencing (scRNA-seq) technology to assess transcriptional heterogeneity between cells in the postnatal day 2 (P2) epithelium and identify distinct epithelial cell subtypes. Analysis of these data was used to better understand lens growth, differentiation, and homeostasis on P2.

Methods

scRNA-seq on P2 mouse lenses was performed using the 10x Genomics Chromium Single Cell 3' Kit (v3.1) and short-read Illumina sequencing. Sequence alignment and preprocessing of data were conducted using 10x Genomics Cell Ranger software. Seurat was employed for preprocessing, quality control, dimensionality reduction, and cell clustering, and Monocle was utilized for trajectory analysis to understand the developmental progression of the lens cells. CellChat and GO analyses were used to explore cell-cell communication networks and signaling interactions.

Results

Lens epithelial cells (LECs) were divided into seven subclusters, classified by specific gene markers. The expression of crystallin, cell-cycle, and metabolic genes was not uniform, indicating distinct functional roles of LECs. Trajectory analysis predicted a bifurcation of differentiating and cycling cells from an Igfbp5+ progenitor pool. We also identified heterogeneity in signaling molecules and pathways, suggesting that cycling and progenitor subclusters have prominent roles in coordinating crosstalk.

Conclusions

scRNA-seq corroborated many known markers of epithelial differentiation and proliferation while providing further insight into the pathways and genes directing these processes. Interestingly, we demonstrated that the developing epithelium can be divided into distinct subpopulations. These clusters reflect the transcriptionally diverse roles of the epithelium in proliferation, signaling, and maintenance.

Single-cell RNA sequencing of neurofibromas reveals a tumor microenvironment favorable for neural regeneration and immune suppression in a neurofibromatosis type 1 porcine model

Neurofibromatosis Type 1 (NF1) is one of the most common genetically inherited disorders that affects 1 in 3000 children annually. Clinical manifestations vary widely but nearly always include the development of cutaneous, plexiform and diffuse neurofibromas that are managed over many years. Recent single-cell transcriptomics profiling efforts of neurofibromas have begun to reveal cell signaling processes. However, the cell signaling networks in mature, non-cutaneous neurofibromas remain unexplored. Here, we present insights into the cellular composition and signaling within mature neurofibromas, contrasting with normal adjacent tissue, in a porcine model of NF1 using single-cell RNA sequencing (scRNA-seq) analysis and histopathological characterization. These neurofibromas exhibited classic diffuse-type histologic morphology and expected patterns of S100, SOX10, GFAP, and CD34 immunohistochemistry. The porcine mature neurofibromas closely resemble human neurofibromas histologically and contain all known cellular components of their human counterparts. The scRNA-seq confirmed the presence of all expected cell types within these neurofibromas and identified novel populations of fibroblasts and immune cells, which may contribute to the tumor microenvironment by suppressing inflammation, promoting M2 macrophage polarization, increasing fibrosis, and driving the proliferation of Schwann cells. Notably, we identified tumor-associated IDO1 +/CD274+ (PD-L1) + dendritic cells, which represent the first such observation in any NF1 animal model and suggest the role of the upregulation of immune checkpoints in mature neurofibromas. Finally, we observed that cell types in the tumor microenvironment are poised to promote immune evasion, extracellular matrix reconstruction, and nerve regeneration.

DeCOOC Deconvoluted Hi-C Map Characterizes the Chromatin Architecture of Cells in Physiologically Distinctive Tissues

Deciphering variations in chromosome conformations based on bulk three-dimensional (3D) genomic data from heterogenous tissues is a key to understanding cell-type specific genome architecture and dynamics. Surprisingly, computational deconvolution methods for high-throughput chromosome conformation capture (Hi-C) data remain very rare in the literature. Here, a deep convolutional neural network (CNN), deconvolve bulk Hi-C data (deCOOC) that remarkably outperformed all the state-of-the-art tools in the deconvolution task is developed. Interestingly, it is noticed that the chromatin accessibility or the Hi-C contact frequency alone is insufficient to explain the power of deCOOC, suggesting the existence of a latent embedded layer of information pertaining to the cell type specific 3D genome architecture. By applying deCOOC to in-house-generated bulk Hi-C data from visceral and subcutaneous adipose tissues, it is found that the characteristic chromatin features of M2 cells in the two anatomical loci are distinctively bound to different physiological functionalities. Taken together, deCOOC is both a reliable Hi-C data deconvolution method and a powerful tool for functional extraction of 3D genome architecture.

Sex-dependent differences in the genomic profile of lingual sensory neurons in naïve and tongue-tumor bearing mice

Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased state of both sexes. Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: (1) FACS sorting obtained higher number of neurons from female trigeminal ganglia (TG) compared to males; (2) Naïve female neurons innervating the tongue expressed immune cell markers such as Csf1R, C1qa and others, that weren't expressed in males. This was validated by Immunohistochemistry. (3) Accordingly, immune cell markers such as Csf1 exclusively sensitized TRPV1 responses in female TG neurons. (4) Male neurons were more tightly regulated than female neurons upon tumor growth and very few differentially expressed genes (DEGs) overlapped between the sexes, (5) Male DEGs contained higher number of transcription factors whereas female DEGs contained higher number of enzymes, cytokines and chemokines. Collectively, this is the first study to characterize the effect of sex as well as of tongue-tumor on global gene expression, pathways and molecular function of tongue-innervating sensory neurons.

Sex-dependent Differences in the Genomic Profile of Lingual Sensory Neurons in Naïve and Tongue-Tumor Bearing Mice

Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased state of both sexes. Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: 1) Tongue tissue of female mice was innervated with higher number of trigeminal neurons compared to males; 2) Naïve female neurons innervating the tongue exclusively expressed immune cell markers such as Csf1R, C1qa and others, that weren't expressed in males. This was validated by Immunohistochemistry. 4) Accordingly, immune cell markers such as Csf1 exclusively sensitized TRPV1 responses in female TG neurons. 3) Male neurons were more tightly regulated than female neurons upon tumor growth and very few differentially expressed genes (DEGs) overlapped between the sexes, 5) Male DEGs contained higher number of transcription factors whereas female DEGs contained higher number of enzymes, cytokines and chemokines. Collectively, this is the first study to characterize the effect of sex as well as of tongue-tumor on global gene expression, pathways and molecular function of tongue-innervating sensory neurons.

Digits in a dish: An in vitro system to assess the molecular genetics of hand/foot development at single-cell resolution

In vitro models allow for the study of developmental processes outside of the embryo. To gain access to the cells mediating digit and joint development, we identified a unique property of undifferentiated mesenchyme isolated from the distal early autopod to autonomously re-assemble forming multiple autopod structures including: digits, interdigital tissues, joints, muscles and tendons. Single-cell transcriptomic analysis of these developing structures revealed distinct cell clusters that express canonical markers of distal limb development including: Col2a1, Col10a1, and Sp7 (phalanx formation), Thbs2 and Col1a1 (perichondrium), Gdf5, Wnt5a, and Jun (joint interzone), Aldh1a2 and Msx1 (interdigital tissues), Myod1 (muscle progenitors), Prg4 (articular perichondrium/articular cartilage), and Scx and Tnmd (tenocytes/tendons). Analysis of the gene expression patterns for these signature genes indicates that developmental timing and tissue-specific localization were also recapitulated in a manner similar to the initiation and maturation of the developing murine autopod. Finally, the in vitro digit system also recapitulates congenital malformations associated with genetic mutations as in vitro cultures of Hoxa13 mutant mesenchyme produced defects present in Hoxa13 mutant autopods including digit fusions, reduced phalangeal segment numbers, and poor mesenchymal condensation. These findings demonstrate the robustness of the in vitro digit system to recapitulate digit and joint development. As an in vitro model of murine digit and joint development, this innovative system will provide access to the developing limb tissues facilitating studies to discern how digit and articular joint formation is initiated and how undifferentiated mesenchyme is patterned to establish individual digit morphologies. The in vitro digit system also provides a platform to rapidly evaluate treatments aimed at stimulating the repair or regeneration of mammalian digits impacted by congenital malformation, injury, or disease.

Identification of Prognostic Aging-Related Genes Associated with Immune Cell Infiltration in Glioblastoma

Background. Aging is recognized as a main tumor risk factor, and thus aging has become a field of interest in the tumor research field. Glioblastoma multiforme represents the most typical primary malignant intracranial tumor, particularly in the elderly. However, the association between aging-related genes (AGs) and GBM prognosis remains unknown. As a result, the primary goal of this study was to determine the association among AGs and the prognosis of GBM. Methods. A total of 307 human AGs were downloaded from the HAGR database, while the expression profiles of GSE4290 and GSE4412 were obtained from the GEO database. Furthermore, data on GBM expression profiles were obtained from the Chinese Glioma Genome Atlas (CGGA) database. The DEAGs that were differentially expressed among the AG and GBM gene expression profiles derived from GSE4290 were then identified, followed by functional analysis of the DEAGs. The survival-related AGs were then screened using univariate Cox regression analysis , which was used to build and validate a prognostic risk model. Furthermore, the ESTIMATE and CIBERSORT algorithms were utilized to explore the association between the survival-related AGs and the tumor immune microenvironment. Results. In entire, 29 DEAGs were identified in the GSE4290. This was monitored by the construction of the prognosis risk model using four DEAGs from the CGGA training set, including C1QA, CDK1, EFEMP1, and IGFBP2. Next, the risk model was confirmed in the CGGA experiment set and the GSE 4412 dataset. Results showed that C1QA, CDK1, EFEMP1, and IGFBP2 levels were remarkably higher in the high-risk score groups, and they had a good association with immune and stromal scores. Conclusion. A robust prognostic risk model was constructed and validated using four AGs, including C1QA, CDK1, EFEMP1, and IGFBP2, which had a close relationship with the immune microenvironment of GBM. This study offers a new reference to further explore the pathogenesis of GBM and recognize new and more effective GBM treatments.

TREM2 as a Prognostic Biomarker for Osteosarcoma Microenvironment Remodeling

The tumor microenvironment (TME) acts as a crucial role in the occurrence and development of osteosarcoma (OS). Despite this, the mechanism controlling the components of immunity and stroma in the tumor microenvironment remains a mystery. To conduct this study, we download and collate transcriptome data from the TARGET database, whose full name is Therapeutically Applicable Research to Generate Effective Treatments, as well as available clinical information of OS. The CIBERSORT and ESTIMATE methodology are used to acquire the proportions of components of immunity and stroma and tumor-infiltrating immune cells (TICs). Protein-protein interaction (PPI) networks and Cox regression analysis are used to select differentially expressed genes (DEGs). A prognostic biomarker is determined by intersecting univariate COX and PPI results, which lead to the finding of Triggering receptor expressed on myeloid cells-2 (TREM2). Based on the next analysis, TREM2 expression is positively correlated with OS survival time. Immune function-related genes have enrichment in the group with high expression of TREM2, according to gene set enrichment analysis (GSEA). The percentage of TICs by CIBERSORT methodology revealed that the expression of TREM2 is positively associated with follicular helper T cells, CD8-positive T cells, and M2 macrophages and negatively correlated with plasma cells, M0 macrophages, and naive CD4-positive T cells. All results suggest a possible integral role of TREM2 in the immune-related events of TME. Therefore, TREM2 may be a potential indicator of remodeling of TME in osteosarcoma, which is useful and helpful in predicting the clinical prognostic outcome of OS patients and provide a unique perspective for immunotherapy for OS.

Dysregulation of innate cell types in the hepatic immune microenvironment of alcoholic liver cirrhosis

Introduction

The risk of alcoholic cirrhosis increases in a dose- and time-dependent manner with alcohol consumption and ethanol metabolism in the liver. Currently, no effective antifibrotic therapies are available. We aimed to obtain a better understanding of the cellular and molecular mechanisms involved in the pathogenesis of liver cirrhosis.

Methods

We performed single-cell RNA-sequencing to analyze immune cells from the liver tissue and peripheral blood form patients with alcoholic cirrhosis and healthy controls to profile the transcriptomes of more than 100,000 single human cells and yield molecular definitions for non-parenchymal cell types. In addition, we performed single-cell RNA-sequencing analysis to reveal the immune microenvironment related to alcoholic liver cirrhosis. Hematoxylin and eosin, Immunofluorescence staining and Flow cytometric analysis were employed to study the difference between tissues and cells with or without alcoholic cirrhosis.

Results

We identified a fibrosis-associated M1 subpopulation of macrophages that expands in liver fibrosis, differentiates from circulating monocytes, and is pro-fibrogenic. We also define mucosal-associated invariant T (MAIT) cells that expand in alcoholic cirrhosis and are topographically restricted to the fibrotic niche. Multilineage modeling of ligand and receptor interactions between the fibrosis-associated macrophages, MAIT, and NK cells revealed the intra-fibrotic activity of several pro-fibrogenic pathways, including responses to cytokines and antigen processing and presentation, natural killer cell-mediated cytotoxicity, cell adhesion molecules, Th1/Th2/Th17 cell differentiation, IL-17 signaling pathway, and Toll-like receptor signaling pathway.

Discussion

Our work dissects unanticipated aspects of the cellular and molecular basis of human organ alcoholic fibrosis at the single-cell level and provides a conceptual framework for the discovery of rational therapeutic targets in liver alcoholic cirrhosis.

F8 gene inversion and duplication cause no obvious hemophilia A phenotype

Hemophilia A (HA, OMIM#306700) is an X-linked recessive bleeding disorder caused by the defects in the F8 gene, which encodes coagulation factor VIII (FVIII). Intron 22 inversion (Inv22) is found in about 45% of patients with severe hemophilia A. Here, we reported a male without obvious hemophilia A phenotype but bearing an inherited segmental variant duplication encompassing F8 as well as Inv22. The duplication was approximately 0.16 Mb and involved from exon 1 to intron 22 of F8. This partial duplication and Inv22 in F8 was first found in the abortion tissue of his older sister with recurrent miscarriage. The genetic testing of his family revealed that his phenotypically normal older sister and mother also had this heterozygous Inv22 and a 0.16 Mb partial duplication of F8, while his father was genotypically normal. The integrity of the F8 gene transcript was verified by sequencing of the adjacent exons at the inversion breakpoint, which explained why this male had no phenotype for hemophilia A. Interestingly, although he had no significant hemophilia A phenotype, the expression of C1QA in his mother, sister, and the male subject was only about half of that in his father and normal population. Our report broadens the mutation spectrum of F8 inversion and duplication and its pathogenicity in hemophilia A.

C1QC, VSIG4, and CFD as Potential Peripheral Blood Biomarkers in Atrial Fibrillation-Related Cardioembolic Stroke

Atrial fibrillation (AF) is a major risk factor for ischemic stroke. We aimed to identify novel potential biomarkers with diagnostic value in patients with atrial fibrillation-related cardioembolic stroke (AF-CE).Publicly available gene expression profiles related to AF, cardioembolic stroke (CE), and large artery atherosclerosis (LAA) were downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified and then functionally annotated. The support vector machine recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO) regression analysis were conducted to identify potential diagnostic AF-CE biomarkers. Furthermore, the results were validated by using external data sets, and discriminability was measured by the area under the ROC curve (AUC). In order to verify the predictive results, the blood samples of 13 healthy controls, 20 patients with CE, and 20 patients with LAA stroke were acquired for RT-qPCR, and the correlation between biomarkers and clinical features was further explored. Lastly, a nomogram and the companion website were developed to predict the CE-risk rate. Three feature genes (C1QC, VSIG4, and CFD) were selected and validated in the training and the external datasets. The qRT-PCR evaluation showed that the levels of blood biomarkers (C1QC, VSIG4, and CFD) in patients with AF-CE can be used to differentiate patients with AF-CE from normal controls (P < 0.05) and can effectively discriminate AF-CE from LAA stroke (P < 0.05). Immune cell infiltration analysis revealed that three feature genes were correlated with immune system such as neutrophils. Clinical impact curve, calibration curves, ROC, and DCAs of the nomogram indicate that the nomogram had good performance. Our findings showed that C1QC, VSIG4, and CFD can potentially serve as diagnostic blood biomarkers of AF-CE; novel nomogram and the companion website can help clinicians to identify high-risk individuals, thus helping to guide treatment decisions for stroke patients.

Strategies to Overcome Resistance to Immune-Based Therapies in Osteosarcoma

Improving the prognosis and cure rate of HGOSs (high-grade osteosarcomas) is an absolute need. Immune-based treatment approaches have been increasingly taken into consideration, in particular for metastatic, relapsed and refractory HGOS patients, to ameliorate the clinical results currently achieved. This review is intended to give an overview on the immunotherapeutic treatments targeting, counteracting or exploiting the different immune cell compartments that are present in the HGOS tumor microenvironment. The principle at the basis of these strategies and the possible mechanisms that HGOS cells may use to escape these treatments are presented and discussed. Finally, a list of the currently ongoing immune-based trials in HGOS is provided, together with the results that have been obtained in recently completed clinical studies. The different strategies that are presently under investigation, which are generally aimed at abrogating the immune evasion of HGOS cells, will hopefully help to indicate new treatment protocols, leading to an improvement in the prognosis of patients with this tumor.

Evidence of Chronic Complement Activation in Asymptomatic Pediatric Brain Injury Patients: A Pilot Study

Physical insult from a mild Traumatic Brain Injury (mTBI) leads to changes in blood flow in the brain and measurable changes in white matter, suggesting a physiological basis for chronic symptom presentation. Post-traumatic headache (PTH) is frequently reported by persons after an mTBI that may persist beyond the acute period (>3 months). It remains unclear whether ongoing inflammation may contribute to the clinical trajectory of PTH. We recruited a cohort of pediatric subjects with PTH who had an acute or a persistent clinical trajectory, each around the 3-month post-injury time point, as well as a group of age and sex-matched healthy controls. We collected salivary markers of mRNA expression as well as brain imaging and psychological testing. The persistent PTH group showed the highest levels of psychological burden and pain symptom reporting. Our data suggest that the acute and persistent PTH cohort had elevated levels of complement factors relative to healthy controls. The greatest change in mRNA expression was found in the acute-PTH cohort wherein the complement cascade and markers of vascular health showed a prominent role for C1Q in PTH pathophysiology. These findings (1) underscore a prolonged engagement of what is normally a healthy response and (2) show that a persistent PTH symptom trajectory may parallel a poorly regulated inflammatory response.

C1QA, C1QB, and GZMB are novel prognostic biomarkers of skin cutaneous melanoma relating tumor microenvironment

Skin cutaneous melanoma (SKCM) is the most lethal form of skin cancers owing to high invasiveness and high metastatic potential. Tumor microenvironment (TME) provides powerful evidences for discerning SKCM, raising the prospect to identify biomarkers of SKCM. Based on the transcriptome profiles of patients with SKCM and the corresponding clinical information from The Cancer Genome Atlas (TCGA), we used ESTIMATE algorithm to calculate ImmuneScore and StromalScore and identified the TME-Related differentially expressed genes (DEGs), than the intersected TME-Related DEGs were used for subsequent functional enrichment analysis. Protein-protein interaction (PPI) analysis was used to identify the functionality-related DEGs and univariate Cox regression analysis was used to identify the survival-related DEGs. Furthermore, SKCM-related DEGs were identified based on two Gene Expression Omnibus (GEO) datasets. Finally, we intersected functionality-related DEGs, survival-related DEGs, and SKCM-related DEGs, ascertaining that six DEGs (CCL4, CXCL10, CCL5, GZMB, C1QA, and C1QB) function as core TME-related genes (CTRGs). Significant differences of GZMB, C1QA, and C1QB expressions were found in gender and clinicopathologic staging of SKCM. High levels of GZMB, C1QA, and C1QB expressions were associated with favorable prognosis. Gene set enrichment analysis (GSEA) showed that cell-cell interaction, cell behavior, and intracellular signaling transduction may be mainly involved in both C1QA, C1QB and GZMB expressions and metabolism of phospholipid and amino acid, transcription, and translation may be implicated in low GZMB expressions. C1QA, C1QB, and GZMB are novel SKCM-relating CTRGs, providing promising immune-related prognostic biomarkers for SKCM.

Multi-omics profiling identifies C1QA/B+ macrophages with multiple immune checkpoints associated with esophageal squamous cell carcinoma (ESCC) liver metastasis

Background

Esophageal squamous cell carcinoma (ESCC) is a highly lethal malignant tumor lacking effective treatments; 20% of ESCC patients develop liver metastasis with an extremely short survival time of ≈5 months. The tumor microenvironment (TME) plays a crucial role in tumor homeostasis, but the relationship between the ESCC TME and liver metastasis is still unknown.

Methods

To identify potential cell populations contributing to ESCC liver metastasis, single-cell RNA (scRNA) sequencing data were analyzed to identify the major cell populations within the TME. Each of the major cell populations was re-clustered to define detailed cell subsets. Thereafter, the gene set variation analysis (GSVA) score was calculated for the bulk RNA-seq data based on the gene signatures of each cell subset. The relationship between the GSVA score of each cellular subset and clinical outcome was further analyzed to identify the cellular subset associated with ESCC liver metastasis, which was validated by multiplex immunohistochemistry.

Results

C1QA/B⁺ tumor-associated macrophages (TAMs) acted as the central regulator of the ESCC TME, closely associated with several key cell subsets. Several immune checkpoints, including CD40, CD47 and LGALS9, were all positively expressed in C1QA/B⁺ macrophages, which may exert central regulatory control of immune evasion by ESCC via these immune checkpoints expressions.

Conclusions

Our results comprehensively revealed the landscape of tumor-infiltrating immune cells associated with ESCC prognosis and metastasis, and suggest a novel strategy for developing immunotherapies for ESCC liver metastasis by targeting C1QA/B⁺ TAMs.

Complement C1QC as a potential prognostic marker and therapeutic target in colon carcinoma based on single-cell RNA sequencing and immunohistochemical analysis

Immune cell infiltration plays an essential role in the occurrence and development of colon cancer. However, the main tumor-associated immune cell infiltration and its gene regulation in colon cancer still need to be further clarified in order to provide a new perspective for diagnosing and treating this disease. For this study, single-cell RNA sequencing (scRNA-seq) expression profiles and TCGA colon cancer data sets were first acquired from the GEO database. Then, Seurat, Monocle, LIMMA, Clusterprofile, GSVA and GSEABase algorithms were used to systematically examine the data. Potential target drugs corresponding to target genes were analyzed in the Drugbank database and detected by molecular docking. Immunohistochemistry was used to assess the level of C1QC expression in the tissue microarray. Single cell analysis suggested that neutrophil activation might be the critical regulatory pathway in colon cancer and that macrophages were the main cell population involved. Subsequent functional enrichment analysis on differential genes in macrophages suggested that C1QC may be a critical regulatory factor in the occurrence and progression of colon cancer, and was closely related to the survival of patients. According to the drug target prediction, palivizumab is a targeted drug for C1QC, and molecular docking demonstrated that palivizumab binds to C1QC. Additionally, tissue-microarray based immunohistochemical analysis showed that C1QC was highly expressed in colon cancer tissue, and the prognosis of colon cancer patients with high C1QC expression was worse, closely related to age, lymphatic metastasis and the TNM stage (Tumor, Nodes and Metastases). Our findings suggest that C1QC may regulate the macrophages in colon cancer immune infiltration, which is expected to be a potential immunotherapy target for colon cancer, and beneficial for the diagnosis and prognosis of colon cancer patients.

Detection of Complement C1q B Chain Overexpression and Its Latent Molecular Mechanisms in Cervical Cancer Tissues Using Multiple Methods

Aim

The aim of this study is to demonstrate the expression and clinicopathological significance of complement C1q B chain (C1QB) in cervical cancer.

Methods

In total, 120 cervical cancer tissues, as well as 20 samples each of high-grade squamous intraepithelial lesions (HSILs), low-grade squamous intraepithelial lesions (LSILs), and benign cervical tissue, were collected to evaluate the expression of C1QB protein via immunohistochemical staining. We conducted an integrated analysis of C1QB mRNA expression in cervical cancer using public microarrays and RNA-seq data sets by calculating standard mean differences (SMDs). Simultaneously, we explored the relations of C1QB with clinicopathological parameters and the expression of P16, Ki-67, and P53.

Results

The expression of C1QB protein was higher in cervical cancer samples than that in benign cervical tissue, LSIL, and HSIL samples (p < 0.05). A combined SMD of 0.65 (95% CI: [0.52, 0.79], p < 0.001) revealed upregulation of C1QB mRNA in cervical cancer. C1QB expression may also be related to the depth of infiltration, lymphovascular invasion, and perineural invasion in cervical cancer (p < 0.05). We also found that C1QB protein expression was positively correlated with P16 and Ki-67 expression in cervical cancer (p < 0.05). The gene set enrichment analysis showed that C1QB may participate in apoptosis and autophagy. A relationship was predicted between C1QB expression and drug sensitivity to cisplatin, paclitaxel, and docetaxel.

Conclusion

We confirmed the overexpression of C1QB in cervical cancer at both mRNA and protein levels for the first time. C1QB may serve as an oncogene in the tumorigenesis of cervical cancer, but this possibility requires further study.

Prognosis-related genes participate in immunotherapy of renal clear cell carcinoma possibly by targeting dendritic cells

Tumor immunotherapy has become one of the most promising approaches to tumor treatment. This study aimed to screen genes involved in the response of clear cell renal cell carcinoma (ccRCC) to immunotherapy and analyze their function. Based on the Gene Expression Omnibus and The Cancer Genome Atlas datasets, we screened out nine differentially expressed genes (TYROBP, APOC1, CSTA, LY96, LAPTM5, CD300A, ALOX5, C1QA, and C1QB) associated with clinical traits and prognosis. A risk signature constructed by these nine genes could predict the survival probability for patients at 1 year, 3 years, and 5 years. The immune checkpoint blockade response rate in the high-risk group was significantly higher than in the low-risk group (49.25% vs. 24.72%, p ≤ 0.001). The nine prognosis-related genes were negatively correlated with activated dendritic cells in the low-risk group but not in the high-risk group. qRT-PCR, immunohistochemistry, and immunofluorescence showed that the nine prognosis-related genes were associated with dendritic cell activity and the PD-1 positive staining rate. In conclusion, the nine prognosis-related genes have a high prognostic value. The patients in the high-risk group were more likely to benefit from immunotherapy, and the mechanism might be related to the release of dendritic cell-mediated immunosuppression.

Single-Cell Transcriptome Analysis Reveals Mesenchymal Stem Cells in Cavernous Hemangioma

A cavernous hemangioma, well-known as vascular malformation, is present at birth, grows proportionately with the child, and does not undergo regression. Although a cavernous hemangioma has well-defined histopathological characteristics, its origin remains controversial. In the present study, we characterized the cellular heterogeneity of a cavernous hemangioma using single-cell RNA sequencing (scRNA-seq). The main contribution of the present study is that we discovered a large number of embryonic mesenchymal stem cells (MSCs) in a cavernous hemangioma and proposed that cavernous hemangiomas may originate from embryonic MSCs. Further analysis of the embryonic MSCs revealed that: 1) proinflammatory cytokines and related genes TNF, TNFSF13B, TNFRSF12A, TNFAIP6, and C1QTNF6 are significantly involved in the MSC-induced immune responses in cavernous hemangiomas; 2) UCHL1 is up-regulated in the embryonic MSC apoptosis induced by proinflammatory cytokines; 3) the UCHL1-induced apoptosis of MSCs may play an important role in the MSC-induced immune responses in cavernous hemangiomas; and 4) UCHL1 can be used as a marker gene to detect embryonic MSCs at different apoptosis stages. In addition to MSCs, ECs, macrophages, T lymphocytes and NKCs were intensively investigated, revealing the genes and pathways featured in cavernous hemangiomas. The present study revealed the origin of cavernous hemangiomas and reported the marker genes, cell types and molecular mechanisms, which are associated with the origin, formation, progression, diagnosis and therapy of cavernous hemangiomas. The better understanding of the MSC-induced immune responses in benign tumours helps to guide future investigation and treatment of embryonic MSC-caused tumours. Our findings initiated future research for the rediscovery of MSCs, cancers/tumours and the UCHL1-induced apoptosis.

Immune Microenvironment in Osteosarcoma: Components, Therapeutic Strategies and Clinical Applications

Osteosarcoma is a primary malignant tumor that tends to threaten children and adolescents, and the 5-year event-free survival rate has not improved significantly in the past three decades, bringing grief and economic burden to patients and society. To date, the genetic background and oncogenesis mechanisms of osteosarcoma remain unclear, impeding further research. The tumor immune microenvironment has become a recent research hot spot, providing novel but valuable insight into tumor heterogeneity and multifaceted mechanisms of tumor progression and metastasis. However, the immune microenvironment in osteosarcoma has been vigorously discussed, and the landscape of immune and non-immune component infiltration has been intensively investigated. Here, we summarize the current knowledge of the classification, features, and functions of the main infiltrating cells, complement system, and exosomes in the osteosarcoma immune microenvironment. In each section, we also highlight the complex crosstalk network among them and the corresponding potential therapeutic strategies and clinical applications to deepen our understanding of osteosarcoma and provide a reference for imminent effective therapies with reduced adverse effects.

AhR Activation Leads to Attenuation of Murine Autoimmune Hepatitis: Single-Cell RNA-Seq Analysis Reveals Unique Immune Cell Phenotypes and Gene Expression Changes in the Liver

The aryl hydrocarbon receptor (AhR) is a ubiquitously expressed ligand-activated transcription factor. While initially identified as an environmental sensor, this receptor has been shown more recently to regulate a variety of immune functions. AhR ligands vary in structure and source from environmental chemicals such as 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and indoles found in cruciferous vegetables to endogenous ligands derived from tryptophan metabolism. In the current study, we used TCDD, a high affinity AhR ligand to study the impact of AhR activation in the murine model of autoimmune hepatitis (AIH). Primarily, we used single-cell RNA-sequencing (scRNA-seq) technology to study the nature of changes occurring in the immune cells in the liver at the cellular and molecular level. We found that AhR activation attenuated concanavalin A (ConA)-induced AIH by limiting chemotaxis of pro-inflammatory immune cell subsets, promoting anti-inflammatory cytokine production, and suppressing pro-inflammatory cytokine production. scRNA-seq analysis showed some unusual events upon ConA injection such as increased presence of mature B cells, natural killer (NK) T cells, CD4+ or CD8+ T cells, Kupffer cells, memory CD8+ T cells, and activated T cells while TCDD treatment led to the reversal of most of these events. Additionally, the immune cells showed significant alterations in the gene expression profiles. Specifically, we observed downregulation of inflammation-associated genes including Ptma, Hspe1, and CD52 in TCDD-treated AIH mice as well as alterations in the expression of migratory markers such as CXCR2. Together, the current study characterizes the nature of inflammatory changes occurring in the liver during AIH, and sheds light on how AhR activation during AIH attenuates liver inflammation by inducing phenotypic and genotypic changes in immune cells found in the liver.

Genetic Cross-Talk between Oral Squamous Cell Carcinoma and Type 2 Diabetes: The Potential Role of Immunity

Background. This bioinformatics study was aimed at evaluating type 2 diabetes (T2D) and oral squamous cell carcinoma (OSCC) with regard to related immune cells and prognosis. Methods. We downloaded the data on OSCC from TCGA and for T2D from GEO database. Differentially expressed genes were analyzed, i.e., for OSCC genes with $p\text{value}<0.01$ , $\left|\log 2\left(\text{FC}\right)\right|>0$ ; and for T2D, genes with $p\text{value}<0.05$ , $\left|\log 2\left(\text{FC}\right)\right|>0$ . The intersected genes between OSCC and T2D were cross-talk genes. The expression values of immune-related genes in case samples in OSCC and T2D were assessed and underwent multivariate and univariate analysis (Cox-PH model). The intersection between the immune genes and cross-talk genes was taken and further analyzed by recursive feature elimination (RFE), survival analysis, and ROC analysis. Results. 1008 cross-talk genes were acquired, including 28 common upregulated, 440 common downregulated, and 540 differently regulated DEGs. We extracted the gene expression value of 782 immune-related genes, of which seven increased immune cells were obtained. From the results, plasmacytoid dendritic cells and effector memory CD8 T cells were highly negatively correlated in both OSCC and T2D. After estimating a low- and high-risk model for survival, we found that activated dendritic cell was significantly different between high and low groups ( $p=0.0095$ ), followed by plasmacytoid dendritic cell. We integrated DE_Immune genes set 1 and DE_Immune genes set 2 and eight key immune-related cross-talk genes (C1QC, ABCD1, NOS2, PDIA4, IL1RN, ALOX15, CSE1L, and PSMC4) were evaluated. After ROC analysis, we obtained that ABCD1, C1QC, CSE1L, and PSMC4 had higher classification and prediction effects on OSCC and T2D. Conclusion. This study revealed a close relationship between T2D and OSCC. Thereby, plasmacytoid dendritic cell and activated dendritic cell-related genes were associated with the survival of T2D-related OSCC, while ABCD1, C1QC, CSE1L, and PSMC4 were the most important immune-related cross-talk genes.

Identification of Cancer-Associated Fibroblast Subtype of Triple-Negative Breast Cancer

Background

There is limited knowledge about the role of cancer-associated fibroblasts (CAF) in the tumor microenvironment of triple-negative breast cancer (TNBC).

Methods

Three hundred and thirty-five TNBC samples from four datasets were retrieved and analyzed. In order to determine the CAF subtype by combining gene expression profiles, an unsupervised clustering analysis was adopted. The prognosis, enriched pathways, immune cells, immune scores, and tumor purity were compared between CAF subtypes. The genes with the highest importance were selected by bioinformatics analysis. The machine learning model was built to predict the TNBC CAF subtype by these selected genes.

Results

TNBC samples were classified into two CAF subtypes (CAF+ and CAF-). The CAF- subtype of TNBC was linked to the longer overall survival and more immune cells than the CAF+ subtype. CAF- and CAF+ were enriched in immune-related pathways and extracellular matrix pathways, respectively. Bioinformatics analysis identified 9 CAF subtype-related markers (ADAMTS12, AEBP1, COL10A1, COL11A1, CXCL11, CXCR6, EDNRA, EPPK1, and WNT7B). We constructed a robust random forest model using these 9 genes, and the area under the curve (AUC) value of the model was 0.921.

Conclusion

The current study identified CAF subtypes based on gene expression profiles and found that CAF subtypes have significantly different overall survival, immune cells, and immunotherapy response rates.

A Complement-Related Gene Signature for Predicting Overall Survival and Immunotherapy Efficacy in Sarcoma Patients

The prognoses of sarcomas are poor and the responses of them to systemic therapies are limited and controversial. Thus, there is an urgent need to stratify the risk factors and identify the patients who may benefit from systemic therapies. Here, we developed a reliable, complement-based gene signature to predict the prognosis of sarcoma patients. Survival-related complement genes were identified by univariate Cox analyses and were used to build a gene signature, which was further selected using the least absolute shrinkage and selection operator model, and determined using a stepwise Cox proportional hazards regression model. The whole sarcoma cohort of TCGA was randomly divided into a training set and a test set. The signature was constructed using the training set and validated subsequently in the test set, the whole TCGA sarcoma cohort, and another two independent cohorts from the TARGET and GEO databases, respectively. Furthermore, the prognostic value of the signature was also validated in an independent cohort from our center. This model effectively predicted prognoses across the training set, different validation cohorts, and different clinical subgroups. Next, immune cell infiltration analysis, GO and KEGG analysis, and gene set enrichment analysis were performed to explore possible underlying mechanisms of this signature. Moreover, this signature may predict the response to immunotherapy. Collectively, the current complement-related gene signature can predict overall survival and possible immunotherapy response of sarcoma patients; it may serve as a powerful prognostic tool to further optimize clinical treatment and prognosis management for sarcoma patients.

Identification of hub genes and transcription factors in patients with rheumatoid arthritis complicated with atherosclerosis

The aim of this study was to explore the overlapping key genes, pathway networks and transcription factors (TFs) related to the pathogenesis of rheumatoid arthritis (RA) and atherosclerosis. The gene expression profiles of RA and atherosclerosis were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between RA and atherosclerosis were identified. The biological roles of common DEGs were explored through enrichment analysis. Hub genes were identified using protein–protein interaction networks. TFs were predicted using Transcriptional Regulatory Relationships Unraveled by Sentence Based Text Mining (TRRUST) database. The hub genes and TFs were validated with other datasets. The networks between TFs and hub genes were constructed by CytoScape software. A total of 131 DEGs (all upregulated) were identified. Functional enrichment analyses indicated that DEGs were mostly enriched in leukocyte migration, neutrophil activation, and phagocytosis. CytoScape demonstrated 12 hub genes and one gene cluster module. Four of the 12 hub genes (CSF1R, CD86, PTPRC, and CD53) were validated by other datasets. TRRUST predicted two TFs, including Spi-1 proto-oncogene (SPI1) and RUNX family transcription factor 1(RUNX1). The expression of RUNX1 was validated with another dataset. Our study explored the common pathogenesis of RA and atherosclerosis. These results may guide future experimental research and clinical transformation.

Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer

BACKGROUND

A growing body of evidence suggests that immune cell infiltration in cancer is closely related to clinical outcomes. However, there is still a lack of research on papillary thyroid cancer (PTC).

METHODS

Based on single-sample gene set enrichment analysis (SSGSEA) algorithm and weighted gene co-expression network analysis (WGCNA) tool, the infiltration level of immune cell and key modules and genes associated with the level of immune cell infiltration were identified using PTC gene expression data from The Cancer Genome Atlas (TCGA) database. In addition, the co-expression network and protein-protein interactions network analysis were used to identify the hub genes. Moreover, the immunological and clinical characteristics of these hub genes were verified in TCGA and GSE35570 datasets and quantitative real-time polymerase chain reaction (PCR). Finally, receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value of hub genes.

RESULTS

Activated B cell, activated dendritic cell, CD56bright natural killer cell, CD56dim natural killer cell, Eosinophil, Gamma delta T cell, Immature dendritic cell, Macrophage, Mast cell, Monocyte, Natural killer cell, Neutrophil and Type 17 T helper cell were significantly changed between PTC and adjacent normal groups. WGCNA results showed that the black model had the highest correlation with the infiltration level of activated dendritic cells. We found 14 hub genes whose expression correlated to the infiltration level of activated dendritic cells in both TCGA and GSE35570 datasets. After validation in the TCGA dataset, the expression level of only 5 genes (C1QA, HCK, HLA-DRA, ITGB2 and TYROBP) in 14 hub genes were differentially expressed between PTC and adjacent normal groups. Meanwhile, the expression levels of these 5 hub genes were successfully validated in GSE35570 dataset. Quantitative real-time PCR results showed the expression of these 4 hub genes (except C1QA) was consistent with the results in TCGA and GSE35570 dataset. Finally, these 4 hub genes had diagnostic value to distinguish PTC and adjacent normal controls.

CONCLUSIONS

HCK, HLA-DRA, ITGB2 and TYROBP may be key diagnostic biomarkers and immunotherapy targets in PTC.

The Complement System in Ovarian Cancer: An Underexplored Old Path

Ovarian cancer is one of the most lethal gynecological cancers. Current therapeutic strategies allow temporary control of the disease, but most patients develop resistance to treatment. Moreover, although successful in a range of solid tumors, immunotherapy has yielded only modest results in ovarian cancer. Emerging evidence underscores the relevance of the components of innate and adaptive immunity in ovarian cancer progression and response to treatment. Particularly, over the last decade, the complement system, a pillar of innate immunity, has emerged as a major regulator of the tumor microenvironment in cancer immunity. Tumor-associated complement activation may support chronic inflammation, promote an immunosuppressive microenvironment, induce angiogenesis, and activate cancer-related signaling pathways. Recent insights suggest an important role of complement effectors, such as C1q or anaphylatoxins C3a and C5a, and their receptors C3aR and C5aR1 in ovarian cancer progression. Nevertheless, the implication of these factors in different clinical contexts is still poorly understood. Detailed knowledge of the interplay between ovarian cancer cells and complement is required to develop new immunotherapy combinations and biomarkers. In this context, we discuss the possibility of targeting complement to overcome some of the hurdles encountered in the treatment of ovarian cancer.