scholarly journals Exploration of the role of tumor mutation burden in clinical significance, immunotherapy response predictor and immune cell infiltration in colon cancer

2020 ◽  
Author(s):  
Zhengshui Xu ◽  
Chao Qu ◽  
Jing Guo ◽  
Xiaopeng Li ◽  
Yunhua Wu ◽  
...  

Abstract Backgroud:Tumor mutation burden has become a powerful bio-marker to predict prognosis and immunotherapy responsiveness to patients in various cancers, but the role of TMB in colon cancer is still unclear.Methods:The transcriptome profiling data of colon patients and the simple nucleotide variation data of colon cases were downloaded from the Cancer Genome Atlas (TCGA) database. The groups were divided into high TMB and low TMB group according to the median of TMB. Then we explored the relationship between immune checkpoints, immune cells and TMB, respectively. Results: Mutation profiles of 399 colon cancer samples were analyzed in TCGA database. The senior (age>65) had a strong relationship with higher-TMB level(p=0.001). Low-TMB group correlated with advanced N stage (P<0.001), M stage (P<0.001), and pathologic stage(P<0.001). High-TMB group had significantly higher mRNA level of PD-L1, TIGIT, HAVCR2, and LAG3 than low-TMB group, which indicated high-TMB referred to better immunotherapy responsiveness in colon cancer. And high-TMB level correlated with higher fractions of CD8T cells (p=0.021), higher CD4 memory T cells(p=0.039), follicular helper T cells (p=0.002)and M1 macrophages (p<0.001), while the low-TMB groups correlated with higher regulator T cells (p=0.002). So high-TMB correlated with stronger immune cell infiltrationConclusions:The high TMB referred to better clinical pathologic features, better immunotherapy responsiveness and stronger immune cells infiltration in colon cancer. Hence TMB may be a very promising bio-marker to predict prognosis and immunotherapy responsiveness to patients in colon cancer.

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shaokun Wang ◽  
Li Pang ◽  
Zuolong Liu ◽  
Xiangwei Meng

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.


2021 ◽  
Author(s):  
Huan Ding ◽  
Huan Hu ◽  
Feifei Tian ◽  
Huaping Liang

The 5-year survival of hepatocellular carcinoma (HCC) is difficult due to the high recurrence rate and metastasis. Tumor infiltrating immune cells (TICs) and immune-related genes (IRGs) bring hope to improve survival and treatment of HCC patients. However, there are problems in predicting immune signatures and identifying novel therapeutic targets. In the study, the CIBERSORT algorithm was used to evaluate 22 immune cell infiltration patterns in gene expression omnibus (GEO) and the cancer genome atlas (TCGA) data. Eight immune cells were found to have significant infiltration differences between the tumor and normal groups. The CD8+ T Cells immune signature was constructed by least absolute shrinkage and selection operator (LASSO) algorithm. The high infiltration level of CD8+ T Cells could significantly improve survival of patients. The weighted gene co-expression network analysis (WGCNA) algorithm identified MMP9 was closely related to the overall survival of HCC patients. K-M survival and tROC analysis confirmed that MMP9 had an excellent prognostic prediction. Cox regression showed that a dual immune signature of CD8+ T Cells and MMP9 was independent survival factor in HCC. Therefore, a dual prognostic immune signature could improve the survival of patient and may provide a new strategy for the immunotherapy of HCC.


2021 ◽  
Vol 12 ◽  
Author(s):  
Zaoqu Liu ◽  
Long Liu ◽  
Dechao Jiao ◽  
Chunguang Guo ◽  
Libo Wang ◽  
...  

Background: Esophageal adenocarcinoma (EAC) remains a leading cause of cancer-related deaths worldwide and demonstrates a predominant rising incidence in Western countries. Recently, immunotherapy has dramatically changed the landscape of treatment for many advanced cancers, with the benefit in EAC thus far been limited to a small fraction of patients.Methods: Using somatic mutation data of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium, we delineated the somatic mutation landscape of EAC patients from US and England. Based on the expression data of TCGA cohort, multiple bioinformatics algorithms were utilized to perform function annotation, immune cell infiltration analysis, and immunotherapy response assessment.Results: We found that RYR2 was a common frequently mutated gene in both cohorts, and patients with RYR2 mutation suggested higher tumor mutation burden (TMB), better prognosis, and superior expression of immune checkpoints. Moreover, RYR2 mutation upregulated the signaling pathways implicated in immune response and enhanced antitumor immunity in EAC. Multiple bioinformatics algorithms for assessing immunotherapy response demonstrated that patients with RYR2 mutation might benefit more from immunotherapy. In order to provide additional reference for antitumor therapy of different RYR2 status, we identified nine latent antitumor drugs associated with RYR2 status in EAC.Conclusion: This study reveals a novel gene whose mutation could be served as a potential biomarker for prognosis, TMB, and immunotherapy of EAC patients.


2021 ◽  
Author(s):  
Ning Huang ◽  
Qiang Chen ◽  
Xiaoyi Wang

Abstract Background Hepatocellular carcinoma (HCC) as malignant cancer has been deeply investigated for its widespread distribution and extremely high mortality rate worldwide. Despite efforts to understand the regulatory mechanism in HCC, it remains largely unknown. Methods The RNA (mRNAs, lncRNAs, and miRNAs) profiles were downloaded from The Cancer Genome Atlas (TCGA) database. Based on the Weighted Gene Co-expression Network Analysis (WGCNA), the hub differentially expressed RNAs (DERNAs) were screened out. The competing endogenous RNA (ceRNA) and Protein and Protein Interaction (PPI) network were constructed based on the hub DERNAs. The Cox and LASSO regression analysis were used to find the independent prognostic ceRNAs. We performed the “CIBERSORT” algorithm estimate the abundance of immune cells. The correlation analysis was applied to determine the relationship between HCC-related immune cells and prognostic ceRNAs. GEPIA and TIMER database were used to explore the association of critical genes with survival and immune cell infiltration, respectively. Results A total of 524 hub RNAs (507 DEmRNAs, 13 DElncRNAs and 4 DEmiRNAs) were identified in the turquoise module (cor = 0.78, P = 4.7e − 198) using WGCNA algorithm. PPI network analysis showed that NDC80, BUB1B and CCNB2 as the critical genes in HCC. Subsequently, survival analysis revealed that the low expression of NDC80 and BUB1B resulted in a longer overall survival (OS) time for HCC patients in GEPIA database. These critical genes and several immune cells were all significantly positive correlated in TIMER database. The ceRNA network were establish, and were incorporated to risk model. Subsequently, ROC curve showed that the area under the curve (AUC) of the 1-, 3-, and 5-year were 0.762, 0.705, and 0.688, respectively. Out of the 22 cell types, T cells CD4 memory resting were identified as the HCC-related immune cells by systematic analysis. The correlation analysis shown that T cells CD4 memory resting is negatively associated with both AL021453.1 (R = − 0.44, P = 0.00049) and CCDC137 (R = − 0.47, P = 2e-04). Conclusion The current study provide potential prognostic signatures and therapeutic targets for HCC.


2021 ◽  
Vol 41 (2) ◽  
Author(s):  
Jie Yu ◽  
QianYun Zhang ◽  
MengChuan Wang ◽  
SiJia Liang ◽  
HongYun Huang ◽  
...  

Abstract Tumor mutation burden (TMB) was a promising marker for immunotherapy. We aimed to investigate the prognostic role of TMB and its relationship with immune cells infiltration in gastric cancer (GC). We analyzed the mutation landscape of all GC cases and TMB of each GC patient was calculated and patients were divided into TMB-high and TMB-low group. Differentially expressed genes (DEGs) between the two groups were identified and pathway analysis was performed. The immune cells infiltration in each GC patient was evaluated and Kaplan–Meier analysis was performed to investigate the prognostic role of immune cells infiltration. At last, hub immune genes were identified and a TMB prognostic risk score (TMBPRS) was constructed to predict the survival outcome of GC patients. The relationships between mutants of hub immune genes and immune infiltration level in GC was investigated. We found higher TMB was correlated with better survival outcome and female patients, patients with T1-2 and N0 had higher TMB score. Altogether 816 DEGs were harvested and pathway analysis demonstrated that patients in TMB-high group were associated with neuroactive ligand–receptor interaction, cAMP signaling pathway, calcium signaling pathway. The infiltration of activated CD4+ memory T cells, follicular helper T cells, resting NK cells, M0 and M1 macrophages and neutrophils in TMB-high group were higher compared than that in TMB-low group and high macrophage infiltration was correlated with inferior survival outcome of GC patients. Lastly, the TMBPRS was constructed and GC patients with high TMBPRS had poor prognosis.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Anila Duni ◽  
Olga Balafa ◽  
George Vartholomatos ◽  
Margarita Oikonomou ◽  
Paraskevi Tseke ◽  
...  

Abstract Background and Aims Advanced chronic kidney disease (CKD) is characterized by elevated expression of the proinflammatory and pro-atherogenic CD14++CD16+ monocytes subset. The role of lymphocyte subpopulations including natural killer (NK) cells and CD4+CD25+ regulatory T cells (Tregs) in the modulation of inflammation and immunity and subsequent cardiovascular implications have received increasing attention. The role of immune cell subpopulations remains to be determined in peritoneal dialysis (PD) patients. The aim of this pilot study was to investigate potential correlations between blood levels of CD14++CD16+ monocytes, NK cells and Tregs with phenotypes of established cardiovascular disease (CVD), including coronary artery disease (CAD) and heart failure (HF) in a cohort of PD patients. Method 29 stable PD patients (mean age 66.96 years ±14.5, 62% males) were enrolled. Exclusion criteria were a history of malignancy, autoimmune disease, active or chronic infections and a recent (< 3 months) cardiovascular event. Demographic, laboratory and bioimpedance measurements data (overhydration, extracellular and total body water and their ratios) were collected. The analysis of peripheral blood immune cell subsets was performed using flow cytometry (FC). Additionally, in 7 PD patients the distribution of the immune cells was evaluated by FC at two time points: T0 (before initiation of PD - CKD stage G5) and T1 (after PD start). Results The median dialysis vintage was 34.5 (range 3.2-141) months. Overall, PD patients had 527 ± 199 monocytes and 1731 ± 489 lymphocytes while mean percentage of CD14++CD16+ monocytes was 9.3 ±6.36% (normal range 2-8%), NK cells 16.6±10.3% (normal range 5-15%) and Tregs 2.1±1.76% (normal range 1-3%). There was no correlation of either of these cell subpopulations with age, PD vintage, inflammation markers (CRP, fibrinogen, albumin, hsTroponin-I), overhydration markers or comorbidities. Only increased NK cells were associated with the presence of HF in PD (24.87 vs 14.92%, p 0.047). In multiple regression analysis, NK cells levels were strongly associated with the presence of edema (beta coef=13.7, p<0.001) and CAD (beta coef=7.1, p=0.046). At T0 mean percentage of CD14++CD16+ monocytes, NK cells and Tregs were 9.7 ±4.5%, 17.1 ±3.84% and 2.38± 1.26% respectively whereas at T1 mean percentage of CD14++CD16+ monocytes was 13.3% ±8.4, NK cells 19.8±6.47% and Tregs 1.5±0.6%. Paired t-test of cell subpopulations (T0 vs T1) showed that only the Tregs were significantly decreased (p =0.018), while the other subpopulations did not differ and remained increased. Conclusion Our study is the first to evaluate the potential association between specific immune cell subsets and cardiovascular disease in long-term PD patients. Increased NK cells levels directly correlate both with the presence of HF and CAD in PD patients. Longitudinal results suggest that CD14++CD16+ and NK cells remain increased after PD start, while Tregs decrease further. The state of pro-inflammation and immune deregulation appear to persist after initiating PD. Future research is required to evaluate the role of immune cells subsets as potential tools to identify patients who are at the highest risk for complications and to guide interventions that may improve clinical outcomes.


Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1380 ◽  
Author(s):  
Haseeb ◽  
Pirzada ◽  
Ain ◽  
Choi

Wnt signaling is one of the important pathways to play a major role in various biological processes, such as embryonic stem-cell development, tissue regeneration, cell differentiation, and immune cell regulation. Recent studies suggest that Wnt signaling performs an essential function in immune cell modulation and counteracts various disorders. Nonetheless, the emerging role and mechanism of action of this signaling cascade in immune cell regulation, as well as its involvement in various cancers, remain debatable. The Wnt signaling in immune cells is very diverse, e.g., the tolerogenic role of dendritic cells, the development of natural killer cells, thymopoiesis of T cells, B-cell-driven initiation of T-cells, and macrophage actions in tissue repair, regeneration, and fibrosis. The purpose of this review is to highlight the current therapeutic targets in (and the prospects of) Wnt signaling, as well as the potential suitability of available modulators for the development of cancer immunotherapies. Although there are several Wnt inhibitors relevant to cancer, it would be worthwhile to extend this approach to immune cells.


2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Henrique Borges da Silva ◽  
Raíssa Fonseca ◽  
José M. Alvarez ◽  
Maria Regina D’Império Lima

Although it has been established that effector memory CD4+T cells play an important role in the protective immunity against chronic infections, little is known about the exact mechanisms responsible for their functioning and maintenance, as well as their effects on innate immune cells. Here we review recent data on the role of IFN-γpriming as a mechanism affecting both innate immune cells and effector memory CD4+T cells. Suboptimal concentrations of IFN-γare seemingly crucial for the optimization of innate immune cell functions (including phagocytosis and destruction of reminiscent pathogens), as well as for the survival and functioning of effector memory CD4+T cells. Thus, IFN-γpriming can thus be considered an important bridge between innate and adaptive immunity.


2021 ◽  
Author(s):  
Jie Mei ◽  
Yun Cai ◽  
Rui Xu ◽  
Xinqian Yu ◽  
Lingyan Chen ◽  
...  

Angiotensin-converting enzyme 2 (ACE2) is known as a host cell receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is identified to be dysregulated in multiple tumors. Although the characterization of abnormal ACE2 expression in malignancies has been preliminarily explored, in-depth analysis of ACE2 in breast cancer (BRCA) has not been elucidated. A systematic pan-cancer analysis was conducted to assess the expression pattern and immunological role of ACE2 based on RNA-sequencing (RNA-seq) data downloaded from The Cancer Genome Atlas (TCGA). Next, correlations between ACE2 expression immunological characteristics in the BRCA tumor microenvironment (TME) were evaluated. Also, the role of ACE2 in predicting the clinical features and the response to therapeutic options in BRCA was estimated. These findings were subsequently validated in another public transcriptomic cohort as well as a recruited cohort. ACE2 was lowly expressed in most cancers compared with adjacent tissues. ACE2 was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), cancer immunity cycles, immune checkpoints, and tumor mutation burden (TMB). Besides, high ACE2 levels indicated the triple-negative breast cancer (TNBC) subtype of BRCA, lower response to endocrine therapy and higher response to chemotherapy, anti-ERBB therapy, antiangiogenic therapy and immunotherapy. To sum up, ACE2 correlates with an inflamed TME and identifies immuno-hot tumors, which may be used as an auxiliary biomarker for the identification of immunological characteristics in BRCA.


2021 ◽  
Vol 9 (Suppl 1) ◽  
pp. A10.2-A11
Author(s):  
S Salmi ◽  
A Lin ◽  
B Hirschovits-Gerz ◽  
M Valkonen ◽  
N Aaltonen ◽  
...  

BackgroundAlthough Malignant Cutaneous Melanoma (CM) is a highly immunogenic cancer, it can evade the immune system by forming an immunosuppressive tumor microenvironment (TME). FoxP3+ Regulatory T cells (Tregs) and indoleamine-2,3-dioxygenase (IDO) are a part of the immunosuppressive TME in CM. In previous studies, IDO expression correlates with poor prognosis and greater Breslow’s depth, but results concerning the role of FoxP3+ Tregs in CM have been controversial. Furthermore, the correlation between IDO and Tregs has not been substantially studied in CM, although IDO is known to be an important regulator of Tregs activity. To develop new therapeutic strategies, it is important to understand the role of immunosuppressive factors in CM.Materials and MethodsWe investigated the associations of FoxP3+ Tregs, IDO+ tumor cells and IDO+ stromal immune cells with tumor stage, prognostic factors, and survival in CM. FoxP3 and IDO were immunohistochemically stained from 29 benign and 29 dysplastic nevi, 18 in situ -melanomas, 48 superficial and 62 deep melanomas and 67 lymph node metastases of CM. The number of FoxP3+ Tregs and IDO+ stromal immune cells was analysed quantitatively and the coverage and intensity of IDO+ tumor cells was evaluated semiquantitatively. Tumors were divided into IDO-negative and IDO-positive, containing less or more than 1% IDO+ melanoma cells of all tumor cells, respectively. P values equal to or less than 0.05 were considered statistically significant.ResultsIDO+ stromal immune cells and FoxP3+ Tregs mainly accumulated in the areas with lymphocyte infiltration and thus resided mostly in the perilesional stroma. The number of FoxP3+ Tregs and IDO+ stromal immune cells were significantly higher in malignant melanomas compared with benign lesions. The increased expression of IDO in melanoma cells was associated with poor prognostic factors, such as recurrence, nodular growth pattern and increased mitotic count. Furthermore, the expression of IDO in melanoma cells was associated with reduced recurrence-free survival. We further showed that IDO-positive tumors contained significantly higher amounts of FoxP3+ Tregs and IDO+ stromal immune cells than IDO-negative tumors. However, the correlation between FoxP3+ Treg and IDO+ stromal immune cell counts was rather weak.ConclusionsOur results indicate that IDO expression is intimately involved in creating a TME conducive to tumor growth in CM. Thus, targeting IDO enzymatic pathway might be a worth of further studies in CM. Furthermore, we show that FoxP3+ Tregs appear to contribute to the immunosuppressive TME in CM, but their role may not be that critical to melanoma progression. The positive association of FoxP3+ Tregs with IDO+ melanoma cells, but not with IDO+ stromal immune cells, indicates a complex interaction between IDO and Tregs in CM, which demands further studies. Support: Sigrid Juselius Foundation (S.P.-S.), Academy of Finland (S.P.-S.), The Paavo Koistinen Foundation (S.S.), Emil Aaltonen Foundation (S.S.) and North-Savo Cultural Foundation (S.S.).Disclosure InformationS. Salmi: None. A. Lin: None. B. Hirschovits-Gerz: None. M. Valkonen: None. N. Aaltonen: None. R. Sironen: None. H. Siiskonen: None. S. Pasonen-Seppänen: None.


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