scholarly journals Elevated N6-Methyladenosine RNA Levels in Peripheral Blood Immune Cells: A Novel Predictive Biomarker and Therapeutic Target for Colorectal Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinye Xie ◽  
Zhijian Huang ◽  
Ping Jiang ◽  
Runan Wu ◽  
Hongbo Jiang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Therapeutic Target ◽  
Immune Cell ◽  
Carbohydrate Antigen ◽  
Pcr Analysis ◽  
Diagnostic Biomarker ◽  
Carbohydrate Antigen 125 ◽  
Rna Levels

Effective biomarkers for the diagnosis of colorectal cancer (CRC) are essential for improving prognosis. Imbalance in regulation of N6-methyladenosine (m6A) RNA has been associated with a variety of cancers. However, whether the m6A RNA levels of peripheral blood can serve as a diagnostic biomarker for CRC is still unclear. In this research, we found that the m6A RNA levels of peripheral blood immune cells were apparently elevated in the CRC group compared with those in the normal controls (NCs) group. Furthermore, the m6A levels arose as CRC progressed and metastasized, while these levels decreased after treatment. The area under the curve (AUC) of the m6A levels was 0.946, which was significantly higher than the AUCs for carcinoembryonic antigen (CEA; 0.817), carbohydrate antigen 125 (CA125; 0.732), and carbohydrate antigen 19-9 (CA19-9; 0.771). Moreover, the combination of CEA, CA125, and CA19-9 with m6A levels improved the AUC to 0.977. Bioinformatics and qRT-PCR analysis further confirmed that the expression of m6A modifying regulator IGF2BP2 was markedly elevated in peripheral blood of CRC patients. Gene set variation analysis (GSVA) implied that monocyte was the most abundant m6A-modified immune cell type in CRC patients’ peripheral blood. Additionally, m6A modifications were negatively related to the immune response of monocytes. In conclusion, our results revealed that m6A RNA of peripheral blood immune cells was a prospective non-invasive diagnostic biomarker for CRC patients and might provide a valuable therapeutic target.

scholarly journals Calculation of immune cell proportion from batch tumor gene expression profile based on support vector regression

2020 ◽  
Vol 18 (05) ◽  
pp. 2050030
Author(s):  
Dongmei Ai ◽  
Gang Liu ◽  
Xiaoxin Li ◽  
Yuduo Wang ◽  
Man Guo
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Support Vector Regression ◽  
Gene Expression Profile ◽  
Immune Cells ◽  
Immune Cell ◽  
Relative Proportion ◽  
Support Vector ◽  
Cancer Tissues ◽  
Cell Proportion

In addition to tumor cells, a large number of immune cells are found in the tumor microenvironment (TME) of cancer patients. Tumor-infiltrating immune cells play an important role in tumor progression and patient outcome. We improved the relative proportion estimation algorithm of immune cells based on RNA-seq gene expression profiling and solved the multiple linear regression model by support vector regression ([Formula: see text]-SVR). These steps resulted in increased robustness of the algorithm and more accurate calculation of the relative proportion of different immune cells in cancer tissues. This method was applied to the analysis of infiltrating immune cells based on 41 pairs of colorectal cancer tissues and normal solid tissues. Specifically, we compared the relative fractions of six types of immune cells in colorectal cancer tissues to those found in normal solid tissue samples. We found that tumor tissues contained a higher proportion of CD8 T cells and neutrophils, while B cells and monocytes were relatively low. Our pipeline for calculating immune cell proportion using gene expression profile data can be freely accessed from GitHub at https://github.com/gutmicrobes/EICS.git.

scholarly journals Comprehensive analysis of tumor microenvironment landscape and potential therapeutic agents based on tumor-infiltrating immune cells in colorectal cancer

2021 ◽  
Author(s):  
Wenhui Zhong ◽  
Feng Zhang ◽  
Xin Lu ◽  
Kaijun Huang ◽  
Junming Bi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Immune Cells ◽  
Transforming Growth Factor ◽  
Immune Cell ◽  
Cancer Therapeutics ◽  
The Cancer Genome Atlas ◽  
Receptor Interaction ◽  
Chemotherapy Drugs ◽  
Drug Compounds

Abstract Background: Tumor-infiltrating immune cells (TIIC) are the major components of the tumor microenvironment (TME) and play vital roles in the tumorigenesis and progression of colorectal cancer (CRC). Increasing evidence has elucidated their significances in predicting prognosis and therapeutic efficacy. Nonetheless, the immune infiltrative landscape of CRC remains largely unknown. Methods: All the RNA-seq transcriptome data and full clinical annotation of 1213 colorectal cancer patients were downloaded from The Cancer Genome Atlas (TCGA) and Gene-Expression Omnibus (GEO) database. The “CIBERSORT” and “estimate” R package were applied to calculate 22 infiltrated immune cell fractions and stromal and immune score. Three TIIC patterns were determined by Unsupervised clustering methods. Through using principal-component analysis, TIIC scores were established. Data for potential agents comes from the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and Cancer Therapeutics Response Portal database (CTRP). Results：In this study, we identified three distinct TIIC patterns characterized by distinct immunological features in 1213 CRC samples from multiple platforms. Base on the TIIC-related gene signatures from three clusters, we constructed a scoring system to quantify the immune infiltration level of individual samples in the CRC cohort and the clinical benefits of different groups. The high TIIC score group was marked by increased immune activation status and favorable prognosis. Conversely, low TIIC score group was featured with immune-desert phenotype and poor prognosis, along with the activation of transforming growth factor-β (TGF-β), WNT, ECM receptor interaction, and VEGF signaling pathways. Meanwhile, the high TIIC score group was also correlated with enhanced efficacy of immunotherapy. Additional, four chemotherapy drugs, seven CTRP-derived drug compounds and six PRISM-derived drug compounds were identified as potential drug for CRC among high and low TIIC subgroups.Conclusions: Collectively, as an effective prognostic biomarker and predictive indicator, the TIIC score plays an important role in the evaluation of CRC prognosis and the response of immunotherapy. Investigation of the TIIC patterns might provide us a promising target for improving immunotherapeutic efficacy in CRC.

scholarly journals SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shaokun Wang ◽  
Li Pang ◽  
Zuolong Liu ◽  
Xiangwei Meng
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Immune Cells ◽  
Immune Cell ◽  
Cox Regression ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
The Relationship

Abstract Background The change of immune cell infiltration essentially influences the process of colorectal cancer development. The infiltration of immune cells can be regulated by a variety of genes. Thus, modeling the immune microenvironment of colorectal cancer by analyzing the genes involved can be more conducive to the in-depth understanding of carcinogenesis and the progression thereof. Methods In this study, the number of stromal and immune cells in malignant tumor tissues were first estimated by using expression data (ESTIMATE) and cell-type identification with relative subsets of known RNA transcripts (CIBERSORT) to calculate the proportion of infiltrating immune cell and stromal components of colon cancer samples from the Cancer Genome Atlas database. Then the relationship between the TMN Classification and prognosis of malignant tumors was evaluated. Results By investigating differentially expressed genes using COX regression and protein-protein interaction network (PPI), the candidate hub gene serine protease inhibitor family E member 1 (SERPINE1) was found to be associated with immune cell infiltration. Gene Set Enrichment Analysis (GSEA) further projected the potential pathways with elevated SERPINE1 expression to carcinogenesis and immunity. CIBERSORT was subsequently utilized to investigate the relationship between the expression differences of SERPINE1 and immune cell infiltration and to identify eight immune cells associated with SERPINE1 expression. Conclusion We found that SERPINE1 plays a role in the remodeling of the colon cancer microenvironment and the infiltration of immune cells.

scholarly journals Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells

2020 ◽  
Author(s):  
Roosheel S. Patel ◽  
Joy E. Tomlinson ◽  
Thomas J. Divers ◽  
Gerlinde R. Van de Walle ◽  
Brad R. Rosenberg
Keyword(s):  
B Cells ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Model Organisms ◽  
Traditional Model ◽  
Cell Type ◽  
Peripheral Blood Mononuclear ◽  
Blood Mononuclear Cells

ABSTRACTTraditional laboratory model organisms represent a small fraction of the diversity of multicellular life, and findings in any given experimental model often do not translate to other species. Immunology research in non-traditional model organisms can be advantageous or even necessary (e.g. for host-pathogen interaction studies), but presents multiple challenges, many stemming from an incomplete understanding of potentially species-specific immune cell types, frequencies and phenotypes. Identifying and characterizing immune cells in such organisms is frequently limited by the availability of species-reactive immunophenotyping reagents for flow cytometry, and insufficient prior knowledge of cell type-defining markers. Here, we demonstrate the utility of single cell RNA sequencing (scRNA-Seq) to characterize immune cells for which traditional experimental tools are limited. Specifically, we used scRNA-Seq to comprehensively define the cellular diversity of equine peripheral blood mononuclear cells (PBMCs) from healthy horses across different breeds, ages, and sexes. We identified 30 cell type clusters partitioned into five major populations: Monocytes/Dendritic Cells, B cells, CD3+PRF1+ lymphocytes, CD3+PRF1- lymphocytes, and Basophils. Comparative analyses revealed many cell populations analogous to human PBMC, including transcriptionally heterogeneous monocytes and distinct dendritic cell subsets (cDC1, cDC2, plasmacytoid DC). Unexpectedly, we found that a majority of the equine peripheral B cell compartment is comprised of T-bet+ B cells; an immune cell subpopulation typically associated with chronic infection and inflammation in human and mouse. Taken together, our results demonstrate the potential of scRNA-Seq for cellular analyses in non-traditional model organisms, and form the basis for an immune cell atlas of horse peripheral blood.

scholarly journals Immune Cell Profiling of Peripheral Blood as Signature for Response During Checkpoint Inhibition Across Cancer Types

2021 ◽  
Vol 11 ◽  
Author(s):  
Vinicius Araujo B. de Lima ◽  
Morten Hansen ◽  
Iben Spanggaard ◽  
Kristoffer Rohrberg ◽  
Sine Reker Hadrup ◽  
...  
Keyword(s):  
Immune Cells ◽  
Peripheral Blood ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Large Fraction ◽  
Response To Treatment ◽  
Cell Phenotype ◽  
Checkpoint Inhibition ◽  
Color Flow ◽  
Immune Profile

Despite encouraging results with immune checkpoint inhibition (ICI), a large fraction of cancer patients still does not achieve clinical benefit. Finding predictive markers in the complexity of the tumor microenvironment is a challenging task and often requires invasive procedures. In our study, we looked for putative variables related to treatment benefit among immune cells in peripheral blood across different tumor types treated with ICIs. For that, we included 33 patients with different solid tumors referred to our clinical unit for ICI. Peripheral blood mononuclear cells were isolated at baseline, 6 and 20 weeks after treatment start. Characterization of immune cells was carried out by multi-color flow cytometry. Response to treatment was assessed radiologically by RECIST 1.1. Clinical outcome correlated with a shift towards an effector-like T cell phenotype, PD-1 expression by CD8+T cells, low levels of myeloid-derived suppressor cells and classical monocytes. Dendritic cells seemed also to play a role in terms of survival. From these findings, we hypothesized that patients responding to ICI had already at baseline an immune profile, here called ‘favorable immune periphery’, providing a higher chance of benefitting from ICI. We elaborated an index comprising cell types mentioned above. This signature correlated positively with the likelihood of benefiting from the treatment and ultimately with longer survival. Our study illustrates that patients responding to ICI seem to have a pre-existing immune profile in peripheral blood that favors good outcome. Exploring this signature can help to identify patients likely to achieve benefit from ICI.

scholarly journals Targeting CXCR4-dependent immunosuppressive Ly6Clow monocytes improves antiangiogenic therapy in colorectal cancer

2017 ◽  
Vol 114 (39) ◽  
pp. 10455-10460 ◽  
Author(s):  
Keehoon Jung ◽  
Takahiro Heishi ◽  
Joao Incio ◽  
Yuhui Huang ◽  
Elizabeth Y. Beech ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Growth ◽  
Immune Cells ◽  
Immune Cell ◽  
Antiangiogenic Therapy ◽  
Innate Immune ◽  
Growth Delay ◽  
Innate Immune Cells ◽  
Tumor Growth Delay ◽  
Anti Vegf

Antiangiogenic therapy with antibodies against VEGF (bevacizumab) or VEGFR2 (ramucirumab) has been proven efficacious in colorectal cancer (CRC) patients. However, the improvement in overall survival is modest and only in combination with chemotherapy. Thus, there is an urgent need to identify potential underlying mechanisms of resistance specific to antiangiogenic therapy and develop strategies to overcome them. Here we found that anti-VEGFR2 therapy up-regulates both C-X-C chemokine ligand 12 (CXCL12) and C-X-C chemokine receptor 4 (CXCR4) in orthotopic murine CRC models, including SL4 and CT26. Blockade of CXCR4 signaling significantly enhanced treatment efficacy of anti-VEGFR2 treatment in both CRC models. CXCR4 was predominantly expressed in immunosuppressive innate immune cells, which are recruited to CRCs upon anti-VEGFR2 treatment. Blockade of CXCR4 abrogated the recruitment of these innate immune cells. Importantly, these myeloid cells were mostly Ly6Clow monocytes and not Ly6Chigh monocytes. To selectively deplete individual innate immune cell populations, we targeted key pathways in Ly6Clow monocytes (Cx3cr1−/− mice), Ly6Chigh monocytes (CCR2−/− mice), and neutrophils (anti-Ly6G antibody) in combination with CXCR4 blockade in SL4 CRCs. Depletion of Ly6Clow monocytes or neutrophils improved anti-VEGFR2–induced SL4 tumor growth delay similar to the CXCR4 blockade. In CT26 CRCs, highly resistant to anti-VEGFR2 therapy, CXCR4 blockade enhanced anti-VEGFR2–induced tumor growth delay but specific depletion of Ly6G+ neutrophils did not. The discovery of CXCR4-dependent recruitment of Ly6Clow monocytes in tumors unveiled a heretofore unknown mechanism of resistance to anti-VEGF therapies. Our findings also provide a rapidly translatable strategy to enhance the outcome of anti-VEGF cancer therapies.

scholarly journals POS0420 DYSREGULATED CD38 EXPRESSION ON PERIPHERAL BLOOD IMMUNE CELL SUBSETS IN SLE

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 439.1-439
Author(s):  
M. Burns ◽  
L. Ostendorf ◽  
A. Grützkau ◽  
F. Hiepe ◽  
T. Alexander ◽  
...  
Keyword(s):  
Immune Cells ◽  
Peripheral Blood ◽  
Plasma Cells ◽  
Immune Cell ◽  
Target Cells ◽  
Type I ◽  
Expression Levels ◽  
Cd38 Expression ◽  
Adaptive Immune Cells ◽  
Hla Dr

Background:Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by pathogenic antinuclear autoantibodies, which are secreted by autoreactive plasma cells. Among novel plasma cell-depleting strategies, CD38 has been identified as promising target. The monoclonal anti-CD38 antibody daratumumab is approved for treatment of multiple myeloma and provided a therapeutically relevant depletion of plasma cells in patients with SLE1.Objectives:Beyond plasma cells, CD38 is widely expressed across innate and adaptive immune cells and additional cellular targets of anti-CD38 treatment, especially in patients with SLE, are largely unknown. Therefore, this study aimed to systematically characterize the expression of CD38 in peripheral blood leukocytes to identify potential target cells of CD38-directed therapies that may contribute to or limit therapeutic benefits in SLE.Methods:We analyzed the expression of CD38 on peripheral blood leukocytes in two different cohorts, comprising a total of 56 SLE patients and 39 healthy controls, by flow and mass cytometry. CD38 expression levels across major immune cells were analyzed for changes between controls and SLE, as well as for correlation across immune cell lineages, and with clinical and serological disease parameters.Results:We detected increased CD38 expression levels on circulating NK cells, plasmacytoid dendritic cells, CD4+ and CD8+ memory T cells, as well as IgD-CD27- and marginal zone-like B cells in SLE compared to healthy controls. In myeloid and NK cells, CD38 expression was associated with an activated cellular phenotype, reflected by co-expression of molecules such as HLA-DR, CD11c or Syk. In the B cell compartment, IgA- plasmablasts and plasma cells expressed more CD38 than their IgA+ counterparts. Also, HLA-DRhigh plasmablasts showed higher CD38 expression compared to HLA-DRlow plasma cells. The strongest differences in CD38 expression between controls and SLE were found in CD8+ central and effector memory T cells. Additionally, we detected an expansion in CD38high and CD38int cells in the T cell memory compartment, with some patients showing distinctly increased expression values. We observed a high intra-individual correlation of CD38 expression across immune cell lineages, yet without correlation of CD38 expression levels with clinical activity (SLEDAI-2K), serological markers of SLE or the type I interferon surrogate marker CD169 (SIGLEC-1).Conclusion:Our data indicate that not only pathogenic plasma cells are potential target cells of CD38-targeting antibodies. The highly dysregulated CD38 expression across innate and adaptive immune cells in SLE could be of pathophysiological importance with respect to the potential efficacy and side effects of such therapies. Since CD38 expression did not correlate with disease activity, it may be assumed that it is not a response protein solely induced and modulated by type I interferons. Nevertheless, our comprehensive characterization of CD38 expression in the immune system might have important implications for personalized approaches with emerging CD38-directed therapeutics.References:[1]Ostendorf, L. et al. Targeting CD38 with Daratumumab in Refractory Systemic Lupus Erythematosus. N. Engl. J. Med. 383, 1149–1155 (2020).Disclosure of Interests:None declared

scholarly journals Analysis of human glioma-associated co-inhibitory immune checkpoints in glioma microenvironment and peripheral blood

2021 ◽  
Vol 35 ◽  
pp. 205873842110565
Author(s):  
Shaoping Shen ◽  
Qiyan Wu ◽  
Jialin Liu ◽  
Liangliang Wu ◽  
Rong Zhang ◽  
...  
Keyword(s):  
Immune Cells ◽  
Peripheral Blood ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Checkpoint Inhibitors ◽  
Myeloid Cell ◽  
Immune Checkpoints ◽  
Human Glioma ◽  
Peripheral Blood Mononuclear ◽  
Glioma Microenvironment

One biomarker for a better therapeutic effect of immune checkpoint inhibitors is high expression of checkpoint in tumor microenvironment The purpose of this study is to investigate the expression of immune checkpoints in human glioma microenvironment and peripheral blood mononuclear cells. First, single-cell suspension from 20 fresh high-grade glioma (HGG) specimens were obtained, and analyzed for lymphocyte composition, then six co-inhibitory immune checkpoints were analyzed at the same time. Second, 36 PBMC specimens isolated from HGG blood samples were analyzed for the same items. In GME, there were four distinct subtypes of cells, among them, immune cells accounted for an average of 51.3%. The myeloid cell population (CD11b+) was the most common immune cell identified, accounting for 36.14% on average; the remaining were most CD3+CD4+ and CD3+/CD8−/CD4− T lymphocytes. In these cells, we detected the expression of BTLA, LAG3, Tim-3, CTLA-4, and VISTA on varying degrees. While in PBMCs, the result showed that when compared with healthy volunteers, the proportion of NK cells decreased significantly in HGG samples ( p < 0.01). Moreover, the expression of BTLA, LAG3, and Tim-3 in CD45+ immune cells in PBMC was more remarkable in glioma samples. In conclusion, the CD11b+ myeloid cells were the predominant immune cells in GME. Moreover, some immune checkpoints displayed a more remarkable expression on the immune cells in GME. And the profile of checkpoint expression in PBMC was partially consistent with that in GME.

scholarly journals Single-Cell Profiling of Kidney Transplant Recipients With Immunosuppressive Treatment Reveals the Dynamic Immune Characteristics

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongguang Liu ◽  
Xiaoyou Liu ◽  
Song Zhou ◽  
Ruiquan Xu ◽  
Jianmin Hu ◽  
...  
Keyword(s):  
T Cells ◽  
Kidney Transplantation ◽  
Cd8 T Cells ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Cd4 T Cells ◽  
Immune Cell ◽  
Immunosuppressive Agents ◽  
Cell Types ◽  
Before And After

Kidney transplantation is currently the first choice of treatment for various types of end-stage renal failure, but there are major limitations in the application of immunosuppressive protocols after kidney transplantation. When the dose of immunosuppressant is too low, graft rejection occurs easily, while a dose that is too high can lead to graft loss. Therefore, it is very important to explore the immune status of patients receiving immunosuppressive agents after kidney transplantation. To compare the immune status of the recipient’s whole peripheral blood before and after receipt of immunosuppressive agents, we used single-cell cytometry by time-of-flight (CyTOF) to detect the peripheral blood immune cells in five kidney transplant recipients (KTRs) from the Department of Organ Transplantation of Zhujiang Hospital of Southern Medical University before and after receiving immunosuppressive agents. Based on CyTOF analysis, we detected 363,342 live single immune cells. We found that the immune cell types of the KTRs before and after receipt of immunosuppressive agents were mainly divided into CD4+ T cells, CD8+ T cells, B cells, NK cells/γδ T cells, monocytes/macrophages, granulocytes, and dendritic cells (DCs). After further reclustering of the above cell types, it was found that the immune cell subclusters in the peripheral blood of patients underwent major changes after receipt of immunosuppressants. After receiving immunosuppressive therapy, the peripheral blood of KTRs had significantly increased levels of CD57+NK cells and significantly decreased levels of central memory CD4+ T cells, follicular helper CD4+ T cells, effector CD8+ T cells, effector memory CD8+ T cells and naive CD8+ T cells. This study used CyTOF to classify immune cells in the peripheral blood of KTRs before and after immunosuppressive treatment, further compared differences in the proportions of the main immune cell types and immune cell subgroups before and after receipt of immunosuppressants, and provided relatively accurate information for assessment and treatment strategies for KTRs.

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