Journal of Peking University (Health Sciences) ›› 2022, Vol. 54 ›› Issue (2): 203-208. doi: 10.19723/j.issn.1671-167X.2022.02.001

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Establishment of a prediction model for colorectal cancer immune cell infiltration based on the cancer genome atlas (TCGA) database

DING Ting-ting,ZENG Chu-xiong,HU Li-na,YU Ming-hua()   

  1. Department of Oncology, Shanghai Pudong Hospital, Pudong Hospital Affiliated to Fudan University, Shanghai 201399, China
  • Received:2021-11-18 Online:2022-04-18 Published:2022-04-13
  • Contact: Ming-hua YU E-mail:ymh3011@163.com
  • Supported by:
    Pudong New Area Science and Technology Development Fund(PKJ2018-Y33);Shanghai Pudong New Area Health System Young Medical Talents Training Program Project(PWRq2021-21)

Abstract:

Objective: To study the correlation between immune cell infiltration in colorectal cancer tissue and clinical prognosis and to explore the levels of some immune cell genes for predicting the prognosis of patients with glioma colorectal cancer. Methods: In this study, we extracted colorectal cancer data from the cancer genome atlas (TCGA). Based on a deconvolution algorithm (called CIBERSORT) and clinically annotated expression profiles, the analysis assessed the infiltration patterns of 22 immune cells in colorectal cancer tissue to determine the association between each cell type and survival. Differences in five-year survival rate effectively illustrate the clinical prognostic value of each immune cell proportion in colorectal cancer, using a bar graph, correlation-based heatmap to represent the proportion of immune cells in each colorectal cancer sample. Results: A total of 473 colorectal cancer tissues and 41 normal control tissues were extracted from the TCGA database, and the comparative analysis showed that there were differences in the proportion of various TIICs in colorectal cancer tissues, which could characterize individual differences and have prognostic value. Among the cell subsets studied, the proportions of memory B cells, plasma cells, CD4+ T cells, natural killer (NK) cells, M0 macrophages, M2 macrophages, and activated mast cells were significantly different between normal and cancer tissues. Resting NK cells, CD8+ T cells, and plasma cells were associated with T phase, activated dendritic cells were associated with N phase, and eosinophils, M1 macrophages, and activated mast cells were associated with M phase. Survival analysis showed that activated dendritic cells were positively associated with five-year survival rate in colorectal cancer patients. Naive CD4+ T cells were inversely associated with five-year survival rate. Conclusion: There are different degrees of immune cell infiltration in colorectal cancer tissues, and these differences may be important determinants of prognosis and treatment response. We conducted a new gene expression-based study of immune cell subtype levels and prognosis in colorectal cancer, which has potential clinical prognostic value in colorectal cancer patients.

Key words: Lymphocytes, tumor-infiltrating, Colorectal neoplasms, Genetic databases, Nomogram, Clinicopathological characteristics

CLC Number: 

  • R730.51

Table 1

General clinical characteristics of colorectal cancer patients in the TCGA database"

Characteristics n (%)
Gender
Male 238 (50.4)
Female 235 (49.6)
Vital status
Living 88 (18.6)
Deceased 385 (81.4)
Clinical stage
StageⅠ-Ⅱ 254 (53.7)
Stage Ⅲ-Ⅳ 219 (46.3)
T stage
T1 10 (2.1)
T2 77 (16.3)
T3 308 (65.1)
T4 78 (16.5)
N stage
N0 270 (57.1)
N1 103 (21.8)
N2 100 (21.1)
M stage
M0 334 (70.6)
M1 62 (23.1)
Mx 77 (16.3)

Figure 1

The proportion of immune cells in each colorectal cancer and normal tissue sample Different colors represent different immune cells, and the length of the bars in the bar graph represents the level of immune cell populations."

Figure 2

Correlation matrix for all 22 TIICs proportions Some immune cells were negatively related, represented in blue, and others were positively related, represented in red. The darker the colour, the higher the correlation was."

Figure 3

Relationship between TIICs and TNM stage and clinical stage of colorectal cancer"

Figure 4

Survival curves of specific immune cell populations with significantly correlated five-year survival rate A, activated dendritic cells; B, naïve CD4+T cells."

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