Alteration in the Immune Microenvironment Based on APC Status in MSS/pMMR Colon Cancer Data Retrieved from TCGA

Abstract BackgroundImmunotherapy is currently the most advanced anti-tumor treatment approach. The efficacy of anti-tumor immunotherapy is closely related to the tumor immune microenvironment, including immune cells, infiltration of immune factors, and expression of immune checkpoints. At present, the biomarkers for predicting the efficacy of colon cancer immunotherapy do not cover all colon cancer patients suitable for immunotherapy. In this study, TCGA database was used to identify tumor genotypes suitable for anti-tumor immunotherapy. MethodsWe downloaded 390 samples with RNA-sequencing data and somatic mutation status data from TCGA. We applied the ESTIMATE, Package limma, the CIBERSORT and some other algorithms to analyze the cellular immune microenvironment. And validated with immunohistochemistry in tumor tissues of colon cancer patients. ResultsWe found that some of the MSS/pMMR populations, that were initially considered unsuitable for immunotherapy, might actually be suitable. In APC-wt/MSS colon cancer, the expression of PD-1, PD-L1, CTLA4 and CYT（GZMA and PRF1）were increased. Based on calculations done by ESTIMATE and CIBERSORT algorithms, the ImmunoScore and the proportion of CT8+ T cell infiltration is increased in these patients. Enrichment analysis was done to screen signaling pathways involved in immune response, extracellular matrix, and cell adhesion. Tumors from 42 colon cancer patients, including 22 APC-mt/MSS and 20 APC-wt/MSS, were immunohistochemically evaluated for expression of CD8 and PD-L1. And APC-wt/MSS tumors showed significantly higher expression of CD8 and PD-L1 than APC-mt/MSS tumor. ConclusionsBased on the results, we found that some colon cancers of APC-wt/MSS are classified by Tumor Immune Microenvironment types (TIMTs) TMIT I. So that we speculate that APC-wt/MSS colon cancer patients could benefit from anti-tumor immunotherapy.

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Alteration in the immune microenvironment based on APC status in MSS/pMMR colon cancer data retrieved from TCGA

10.21203/rs.3.rs-56379/v1 ◽

2020 ◽

Author(s):

Haishan Lin ◽

Hongchao Zhen ◽

Kun Shan ◽

Xiaoting Ma ◽

Bangwei Cao

Keyword(s):

Colon Cancer ◽

Cancer Patients ◽

Enrichment Analysis ◽

Tumor Immunotherapy ◽

Immune Checkpoints ◽

Immune Microenvironment ◽

Cancer Data ◽

T Cell Infiltration ◽

Colon Cancers ◽

Tumor Immune Microenvironment

Abstract Immunotherapy is currently the most advanced anti-tumor treatment approach. The efficacy of anti-tumor immunotherapy is closely related to the tumor immune microenvironment, including immune cells, infiltration of immune factors, and expression of immune checkpoints. At present, the biomarkers for predicting the efficacy of colon cancer immunotherapy do not cover all colon cancer patients suitable for immunotherapy. In this study, TCGA database was used to identify tumor genotypes suitable for anti-tumor immunotherapy. We found that some of the MSS/pMMR populations, that were initially considered unsuitable for immunotherapy, might actually be suitable. In APC-wt/MSS colon cancer, the expression of PD-1, PD-L1, CTLA4 and CYT（GZMA and PRF1）were increased. Based on calculations done by ESTIMATE and CIBERSORT algorithms, the ImmunoScore and the proportion of CT8+ T cell infiltration is increased in these patients. Enrichment analysis was done to screen signaling pathways involved in immune response, extracellular matrix, and cell adhesion. Tumors from 42 colon cancer patients, including 22 APC-mt/MSS and 20 APC-wt/MSS, were immunohistochemically evaluated for expression of CD8 and PD-L1. And APC-wt/MSS tumors showed significantly higher expression of CD8 and PD-L1 than APC-mt/MSS tumor. Based on the results, we found that some colon cancers of APC-wt/MSS are classified by Tumor Immune Microenvironment types (TIMTs) TMIT I. So that we speculate that APC-wt/MSS colon cancer patients could benefit from anti-tumor immunotherapy.

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Uncovering the immune-modulating role of anti-RANKL therapy for cervical cancer: Preliminary results.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e18028 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e18028-e18028

Author(s):

Peter Van Dam ◽

Yannick Verhoeven ◽

Jorrit De Waele ◽

Julie Jacobs ◽

Pieter-Jan Van Dam ◽

...

Keyword(s):

Cervical Cancer ◽

Rna Sequencing ◽

Immune Checkpoints ◽

Clinicopathological Parameters ◽

Sequencing Data ◽

Immune Microenvironment ◽

Preliminary Results ◽

Risk Of Death ◽

Increased Risk ◽

Tumor Immune Microenvironment

e18028 Background: Conventional treatments for cervical cancer (CC) have reached a plateau and only limited progress for targeted therapy has been made over the last decades, resulting in a meager five-year survival rate of only 17% for the advanced stages. To improve long-term benefits for the patient, a promising hot field of research in oncology that opens new perspectives is immunotherapy. Even though CC has shown to be immunogenic, only a minority of patients respond to this type of treatment. In recent years, the RANKL/RANK signaling pathway has been implicated as a key immune modulating factor in the tumor microenvironment, allowing the cancer cells to evade the immune response by disrupting the immune-intrinsic crosstalk. Both RANKL and RANK are highly co-expressed in CC, which correlates with inferior clinicopathological parameters and an increased risk of death. Targeting this pathway may therefore be of great value in the treatment of CC and the quest to release the brakes on the immune system, thereby reinvigorating the tumors’ susceptibility to immunotherapy. Hence, we aim to elucidate the effects of anti-RANKL therapy on the tumor-immune microenvironment in CC. Methods: Two cervical biopsies were taken before and after anti-RANKL therapy in CC patients. One fresh biopsy was immediately processed to a single cell suspension for flow cytometry (FCM) using enzymatic digestion, while the other was formalin-fixed and paraffin-embedded for immunohistochemistry (IHC) and RNA sequencing. For FCM and IHC, the samples were stained with different markers for RANK/L signaling, the immune infiltrate and immune checkpoints. FCM was performed on a BD FACSAria IIä cytometer and analyzed with FlowJo. IHC staining was performed on a Ventana Benchmark Ultra and Ventana Discovery Ultra and scored by a pathologist or by HistoScientist using Visiopharm, while RNA sequencing was performed with the Truseq RNA exome panel on the NextSeq 500 system. Results: Our preliminary results show a relative increase of the CD8+ population, while a trend is observed in increased lymphocyte activation after anti-RANKL therapy. Updated results will be presented in more detail at the conference, including RNA sequencing data. Conclusions: Preliminary findings indicate that anti-RANKL therapy modifies the tumor-immune microenvironment in CC. Higher patient accrual will allow to dissect targets for combination therapy with anti-RANKL to further optimize this treatment strategy.

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TGFβ1: an Indicator for Tumor Immune Microenvironment (TIME) of Colon Cancer from a Comprehensive Analysis of TCGA

10.21203/rs.3.rs-69238/v1 ◽

2020 ◽

Author(s):

Jinyan Wang ◽

Jinqiu Wang ◽

Quan Gu ◽

Yan Yang ◽

Yajun Ma ◽

...

Keyword(s):

Colon Cancer ◽

Cox Regression ◽

Enrichment Analysis ◽

Ppi Network ◽

Immune Microenvironment ◽

Cox Regression Analysis ◽

Difference Analysis ◽

Stromal Component ◽

Tumor Immune Microenvironment ◽

The Difference

Abstract Background: Tumor microenvironment (TME) and tumor-infiltrating immune cells (TIC) greatly participated in the genesis and development of colon cancer (CC). However, there are few researches exploring the dynamic modulation of TME. Methods: In our study, we analyzed the proportion of immune/stromal component and TIC in TME of 473 CC samples and 41 normal samples from The Cancer Genome Atlas (TCGA) database through ESTIMATE and CIBERSORT algorithm. Correlation analysis was carried out to evaluate the association between immune/stromal component in TME and clinicopathological characteristics of CC patients. The difference analysis was performed to obtain the differentially expressed genes (DEGs). These DEGs were further analyzed by gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses, protein–protein interaction (PPI) network construction and COX regression analysis. Transforming growth factor β1 (TGFβ1) was finally overlapping from the above analysis. Furthermore, TGFβ1 was analyzed by paired analysis, Gene Set Enrichment Analysis (GSEA). The intersection between the difference analysis and correlation analysis was also conducted to learn the association between TGFβ1 and TICs.Results: Our result showed that immune component in TME was negatively related with the stages of CC. GO and KEGG enrichment analysis revealed that 1110 DEGs obtained from difference analysis were mainly enriched in immune-related activities. The intersection analysis between PPI network and COX regression analysis indicted that TGFβ1 was significantly associated with the communication of genes in PPI network and the Hazard Ratio (HR) of CC patients’ survival. In addition, TGFβ1 was up-regulated in the tumor samples and significantly related with poor prognosis of CC patients. Further GSEA suggested that genes in TGFβ1 up-regulated group were primarily enriched in immune-related activities and the function of TGFβ1 might depend on the communications with TICs, including T cells CD4 naïve and T cells regulatory (Tregs). Conclusions: The expression of TGFβ1 might be an indicator for tumor immune microenvironment (TIME) of CC and sever as a prognostic factor of CC. Drugs targeting TGFβ1 might be a potential immunotherapy for CC patients in the future.

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P02.07 Characterization of the tumor immune microenvironment of pediatric posterior fossa A ependymomas

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2021-itoc8.19 ◽

2021 ◽

Vol 9 (Suppl 1) ◽

pp. A10.1-A10

Author(s):

J Lammers ◽

F Calkoen ◽

M Kranendonk ◽

A Federico ◽

M Kool ◽

...

Keyword(s):

Rna Sequencing ◽

Posterior Fossa ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Rna Expression ◽

Sequencing Data ◽

Immune Microenvironment ◽

Gene Set Enrichment ◽

Tumor Immune Microenvironment ◽

Immune Related Genes

BackgroundEpendymoma is the third most common brain tumor in children. At the moment, surgery and radiotherapy are the only effective treatments that can be offered, and despite this, a significant part of the patients relapse with no therapeutic salvage options. Therefore, new treatment modalities are needed. To develop immunotherapies for these children, knowledge of the tumor microenvironment is crucial. The current study aims to unravel the tumor immune microenvironment (TIME) of pediatric posterior fossa A (PFA) ependymomas.Materials and MethodsWe used bulk RNA sequencing data of 22 pediatric ependymomas. We defined two groups, hereafter called PFA immune+ (PFAI+) and PFAI-, based on the RNA expression levels of the NanoString panel of Human PanCancer Immune Profiling genes. We performed gene set enrichment analysis and deconvoluted the bulk RNA samples with ependymoma-specific single-cell RNA sequencing datasets. To validate our findings on a protein level, we applied immunohistochemistry with antibodies recognizing tumor-infiltrating lymphocytes, tumor-associated macrophages and microglia.ResultsUnsupervised hierarchical clustering of RNA expression of immune-related genes revealed two distinct PFA groups. Differential gene expression analysis showed that PFAI+ have a significantly higher expression of genes associated with immune functions, such as CD3E, CCR2, GZMA, CXCL9 and TRBC2. Accordingly, gene set enrichment analysis demonstrated that several immune pathways, including T-cell signalling, interferon-gamma response and TNFα signalling are enriched in PFAI+ ependymomas. RNA expression of immune checkpoints was also higher in PFAI+ tumors, indicating that these tumors might be more responsive to combinational therapies including immune checkpoint inhibitors. While immunohistochemistry showed low amounts of infiltrating CD3+, CD8+ and CD20+ cells, high numbers of CD163+ and HLA-DRA+ cells were detected. These cells were mainly located in regions of tumor necrosis. Increased amounts of CD4+ and CD8+ lymphocytes were present in PFAI+ tumors compared to PFAI- tumors. Deconvolution of the bulk RNA samples based on single-cell RNA sequencing data revealed an enrichment of myeloid cell populations, especially microglia and macrophages. Furthermore, PFAI+ tumors were found to contain significantly higher relative proportions of T-cells compared to PFAI- tumors (median of 3.76% for PFAI+ compared to 0.03% for PFAI-).ConclusionsWe suggest that pediatric posterior fossa A ependymomas can be divided into two groups based on the expression of immune-related genes, in which PFAI+ ependymomas are characterized by higher RNA expression levels of these genes and greater amounts of tumor-infiltrating immune cells. Several techniques showed an enrichment of T-lymphocytes in the PFAI+ ependymomas relative to the PFAI- ependymomas.Disclosure InformationJ. Lammers: None. F. Calkoen: None. M. Kranendonk: None. A. Federico: None. M. Kool: None. L. Kester: None. J. van der Lugt: None.

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151 - Colonic Bacteria and the Tumor Immune Microenvironment of Colorectal Cancer Patients

Gastroenterology ◽

10.1016/s0016-5085(18)30609-7 ◽

2018 ◽

Vol 154 (6) ◽

pp. S-41

Author(s):

Jada C. Domingue ◽

Nicolas Llosa ◽

James White ◽

Julia L. Drewes ◽

Christine Craig ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Patients ◽

Immune Microenvironment ◽

Colonic Bacteria ◽

Tumor Immune Microenvironment ◽

Colorectal Cancer Patients

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Comparing of pan-cancer tumor immune microenvironment.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e15100 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e15100-e15100

Author(s):

Jiaan Ye ◽

Longgang Cui ◽

Xiaochen Zhao ◽

Guanghui Lan

Keyword(s):

Colorectal Cancer ◽

T Cells ◽

Natural Killer Cell ◽

Natural Killer ◽

Cancer Patients ◽

Killer Cell ◽

Immune Microenvironment ◽

Hepatobiliary Cancer ◽

Tumor Immune Microenvironment ◽

Pan Cancer

e15100 Background: Cancer treatment has entered the era of immune checkpoint inhibitors (ICI), but different tumors have different responses to ICI drugs. For example, non-small cell lung cancer and melanoma have higher response rates to ICIs than colorectal cancer and liver cancer patients. Previous studies have shown that tumor immune microenvironment have a great impact on the efficacy of ICI. Methods: This study retrospectively included pan-cancer patient specimens, using multiple fluorescent labeling immunohistochemistry to explore the differences in the immune microenvironment of different tumors. Shapiro-Wilk was used for normality test, and ANOVA or Kruskal Wallis test was used according to the results. Two-sided P < 0.05 was considered a significant difference. Results: The study included 308 patients, including 119 (38.6%) NSCLC patients, 72 (23.4%) Colorectal cancer patients, 51 (16.6%) Hepatobiliary cancer patients and 66 (21.4%) Others types of cancer patients. Among them, there was 192 (62.3%) Male, and 116 (37.7%) Female, and the median age was 57 (50-66). The proportion of CD8+ T cells and natural killer cell in tumor was statistically different. The proportion of CD8+ T cells in NSCLC, Colorectal cancer, Hepatobiliary cancer and others was 2.16%, 1%, 1.77% and 2.63%, p < 0.01; the proportion of natural killer cell was 16.44 %, 4.91%, 5.58% and 3.29%, p < 0.01. Conclusions: Different tumor types have different immune microenvironments. These results may provide valuable clues for future ICI trail design.

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Can Intratumoral neutrophil lymphocyte ratio (NLR) be a prognostic biomarker in breast cancer patients?

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e12573 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e12573-e12573

Author(s):

Yoshihisa Tokumaru ◽

Masanori Oshi ◽

Vijayashree Murthy ◽

Eriko Katsuta ◽

Nobuhisa Matsuhashi ◽

...

Keyword(s):

Breast Cancer ◽

T Cells ◽

Cancer Patients ◽

Immune Cells ◽

Breast Cancer Patients ◽

Immune Microenvironment ◽

High Group ◽

Anti Cancer ◽

Tumor Immune Microenvironment ◽

Er Positive

e12573 Background: In breast cancer patients, it is well known that the elevation of neutrophil lymphocyte ratio (NLR) in the blood are reported to associate with poor prognosis based on the notion that neutrophils represent pro-cancer, and lymphocytes represent anti-cancer immune cells. Tumor immune microenvironment has been demonstrated to play critical roles in the outcome of breast cancer patients. However, there is scarce evidence on the clinical relevance of intratumoral NLR in breast cancer patients. In the current study, we hypothesized that intratumoral NLR high tumors are associated with worse survival particularly in TNBC that is known to have high immune cell infiltration. Methods: A total of 1904 breast cancer patients’ data from METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) and analyzed. NLR was calculated by the gene expressions of CD66b (CEACAM8) and CD8 (CD8A). NLR high and low were divided by the median. Overall Survival (OS) and Disease-Free Survival were calculated utilizing Kaplan Meier method between intratumoral NLR high and low groups. xCell algorithm was used to analyze the infiltrated immune cells within the tumor immune microenvironment as we have previously published. Results: Intratumoral NLR high group was associated with worse OS in whole, ER-positive/HER2-negative, and triple negative (TN) subtypes, in agreement with the previous studies. TN subtype alone demonstrated worse DFS of NLR high group. Surprisingly, gene set enrichment analysis (GSEA) demonstrated no gene set enrichment to NLR high group, which implicates that there is no distinctive mechanism that associate with worse survival. Whereas, immune response-related gene sets significantly enriched to NLR low group in TN subtype. This enrichment was consistent in ER-positive/HER2-negative. Compared with ER-positive/HER2-negative subtype, anti-cancer immune cells such as CD4+ T cells, CD8+ T cells, M1 macrophage, and helper T helper type 1 cells were significantly infiltrated in TN patients (p < 0.001 for all genes), where M2 macrophages and neutrophils were less and regulatory T cells and T helper type 2 cells were more infiltrated in TN subtype. Furthermore, intratumoral NLR was significantly lower in TN compared with ER-positive/HER2-negative subtype (p < 0.001). These results suggest that intratumoral NLR low group is associated with better survival due to favorable tumor immune microenvironment in TN subtype rather than NLR high group has worse survival. Conclusions: Intratumoral NLR low tumor demonstrated more favorable OS and more favorable DFS in TN patients. Intratumoral NLR low breast cancer was associated with enhanced immune response and higher infiltration of anti-cancer immune cells were observed in TN subtype compared to ER-positive/HER2-negative which may contribute to the favorable outcome of in TN breast cancer.

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Analysis of multi-omics differences in left-side and right-side colon cancer

PeerJ ◽

10.7717/peerj.11433 ◽

2021 ◽

Vol 9 ◽

pp. e11433

Author(s):

Yanyi Huang ◽

Jinzhong Duanmu ◽

Yushu Liu ◽

Mengyun Yan ◽

Taiyuan Li ◽

...

Keyword(s):

Colon Cancer ◽

Cancer Patients ◽

Gene Mutation ◽

Somatic Mutation ◽

Transcriptome Data ◽

Characteristic Analysis ◽

Immune Microenvironment ◽

Mutation Data ◽

Upregulated Genes ◽

Testing Set

Background Colon cancer is one of the most common tumors in the digestive tract. Studies of left-side colon cancer (LCC) and right-side colon cancer (RCC) show that these two subtypes have different prognoses, outcomes, and clinical responses to chemotherapy. Therefore, a better understanding of the importance of the clinical classifications of the anatomic subtypes of colon cancer is needed. Methods We collected colon cancer patients’ transcriptome data, clinical information, and somatic mutation data from the Cancer Genome Atlas (TCGA) database portal. The transcriptome data were taken from 390 colon cancer patients (172 LCC samples and 218 RCC samples); the somatic mutation data included 142 LCC samples and 187 RCC samples. We compared the expression and prognostic differences of LCC and RCC by conducting a multi-omics analysis of each using the clinical characteristics, immune microenvironment, transcriptomic differences, and mutation differences. The prognostic signatures was validated using the internal testing set, complete set, and external testing set (GSE39582). We also verified the independent prognostic value of the signature. Results The results of our clinical characteristic analysis showed that RCC had a significantly worse prognosis than LCC. The analysis of the immune microenvironment showed that immune infiltration was more common in RCC than LCC. The results of differential gene analysis showed that there were 360 differentially expressed genes, with 142 upregulated genes in LCC and 218 upregulated genes in RCC. The mutation frequency of RCC was generally higher than that of LCC. BRAF and KRAS gene mutations were the dominant genes mutations in RCC, and they had a strong mutual exclusion with APC, while APC gene mutation was the dominant gene mutation in LCC. This suggests that the molecular mechanisms of RCC and LCC differed. The 4-mRNA and 6-mRNA in the prognostic signatures of LCC and RCC, respectively, were highly predictive and may be used as independent prognostic factors. Conclusion The clinical classification of the anatomic subtypes of colon cancer is of great significance for early diagnosis and prognostic risk assessment. Our study provides directions for individualized treatment of left and right colon cancer.

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