Abstract
Introduction
APC and TP53 are the two most regularly mutated genes in colon adenocarcinoma (COAD), especially in progressive malignancies and antitumoral immune response. The current bioinformatics analysis investigates the APC and TP53 gene expression profile in colon adenocarcinoma as a prognostic characteristic for survival, particularly concentrating on the correlated immune microenvironment.
Methods
Clinical and genetic data of colon cancer and normal tissue samples were obtained from The Cancer Genome Atlas (TCGA)-COAD and Genotype-Tissue Expression (GTEx) online databases, respectively. The genetic differential expressions were analyzed in both groups via the one-way ANOVA test. Kaplan–Meier survival curves were applied to estimate the overall survival (OS). P < 0.05 was fixed as statistically significant. On Tumor Immune Estimation Resource and Gene Expression Profiling Interactive Analysis databases, the linkage between immune cell recruitment and APC and TP53 status was assessed through Spearman's correlation analysis.
Results
APC and TP53 were found mutated in 66.74% and 85.71% of the 454 and 7 TCGA-COAD patients in colon and rectosigmoid junction primary sites, respectively with a higher log2-transcriptome per million reads compared to the GTEx group (318 samples in sigmoid and 368 samples in transverse). Survival curves revealed a worse significant OS for the high-APC and TP53 profile colon. Spearman's analysis of immune cells demonstrated a strong positive correlation between the APC status and infiltration of T cell CD4+, T cell CD8+, NK cell, and macrophages and also a positive correlation between status and infiltration of T cell CD4+, T cell CD8+.
Conclusions
APC and TP53 gene mutations prevail in colon cancer and are extremely associated with poor prognosis and shortest survival. The infiltrating T cell CD4+, T cell CD8+, NK cell, and macrophages populate the colon microenvironment and regulate the mechanisms of tumor advancement, immune evasion, and sensitivity to standard chemotherapy. More comprehensive research is needed to demonstrate these results and turn them into new therapeutic outlooks.
Introduction
The second most frequently diagnosed malignancy worldwide and the major cause of cancer-associated deaths is colon adenocarcinoma (COAD). Presently, surgery, radiotherapy, and chemotherapy are the main COAD treatment options [1].
COAD is characterized by frequent mutations of various genes especially in the adenomatous polyposis coli (APC) and tumor protein 53 (TP53) genes. These mutations have been shown to play a crucial role in tumor progression and the modulation of antitumoral immune responses. Understanding the immune landscape and its correlation with the genetic alterations in COAD is essential for identifying prognostic markers and potential therapeutic targets [2–4]. These genetic variations are believed to contribute to various characteristics of colon cancer cells, including stemness, proliferation, dedifferentiation, impaired genome maintenance, invasiveness, and metastatic potential [5–7].
The adenomatous polyposis coli (APC) gene has been recognized as a tumor suppressor gene in colon adenocarcinoma (COAD), and its dysregulation occurs at both the germline and somatic levels. Situated on chromosome 5q21-q22, the APC gene spans 8,535 nucleotides and encompasses 21 exons. Encoding a 310 kDa protein comprising 2,843 amino acids, the APC gene's coding sequence is predominantly located on exon 15, which is the most frequently affected region in both germline and somatic APC mutations [8]. Germ-line mutations in the APC gene give rise to familial adenomatous polyposis (FAP), a significant hereditary predisposition to the development of colon adenocarcinoma. Somatic APC mutations are present in more sporadic colon adenocarcinomas, and loss of heterozygosity (LOH) of chromosome 5q is observed in some of COAD cases [9]. APC is a multi-domain protein with diverse functions facilitated by interactions with various binding partners. Starting from the N terminus to the C terminus, it consists of an oligomerization domain, an armadillo repeat domain, a 15 or 20 residue repeat domain, a SAMP repeats domain, a basic domain, and C-terminal domains [10]. These residues repeat domain and SAMP repeats play crucial roles in suppressing the canonical Wnt signaling pathway by promoting proteasomal degradation of β-catenin. The basic and C-terminal domains, which interact with microtubules directly or indirectly via EB1, are essential for microtubule stabilization, kinetochore functions, and chromosomal segregation. Due to its interactions with various proteins, APC participates in cellular processes encompassing cell migration, adhesion, proliferation, differentiation, and chromosome segregation [11]. The role of APC mutation in the development and advancement of COAD, characterized by heightened proliferation and reduced differentiation of intestinal epithelial cells, has been extensively demonstrated [12]. Nonetheless, there is a relative scarcity of research examining the correlation between APC mutations in COAD and the effectiveness of immunotherapy.
Among the frequently mutated genes, TP53 plays a crucial role in the development of COAD [13]. TP53 encodes the well-known tumor suppressor protein p53, which triggers cell-cycle arrest, senescence, or apoptosis in response to cellular stressors like DNA damage, hypoxia, nutrient depletion, and oncogenic signaling [14]. Through the regulation of target molecules such as p21, Tiger, and PAI-1, p53 facilitates these cellular responses. TP53 variations can be categorized as missense variations or nonsense/frameshift variations. Loss-of-function variations in TP53 lead to tumorigenesis due to reduced induction of p53 targets during cellular stress [15]. Moreover, accumulating evidence suggests that missense-type variations occurring in the DNA binding domain of TP53 can confer oncogenic properties [16].
In this study, we performed a comprehensive bioinformatic analysis to investigate the expression profiles of APC and TP53 genes in colon adenocarcinoma and their prognostic implications. We focused on assessing the immune microenvironment and its relationship with these genetic alterations.
Materials and methods
Data acquisition
Genetic, transcriptomes, and clinical features of colon adenocarcinoma patients were extracted from The Cancer Genome Atlas (TCGA)-COAD project (https://portal.gdc.cancer.gov) (accessed on 19 September 2023) [17]. The TCGA-COAD project is a comprehensive database that provides valuable genomic and clinical information for cancer research.
In addition to the TCGA-COAD project, genetic data from normal colon tissue samples was obtained from the Genotype-Tissue Expression (GTEx) online database (https://gtexportal.org) (accessed on 25 September 2023). The GTEx database is a valuable resource that provides gene expression data across various tissues and helps understand the normal patterns of gene expression.
By leveraging these two reputable sources, the study was able to acquire the necessary genetic, transcriptomic, and clinical data to investigate colon adenocarcinoma comprehensively. This robust data acquisition process ensures the reliability and accuracy of the subsequent analyses and findings.
Analysis of immune infiltrating cells
In the investigation of the immune microenvironment within the colon, particular attention was given to the TCGA-COAD cohort. The study focused on analyzing the presence and characteristics of specific immune cell types, such as T cells CD4+, CD8+, NK cells, and macrophages.
To explore the relationship between the mRNA expression of the APC and TP53 genes and the transcriptional profile of each tumor immune cell, the researchers utilized a powerful tool called Tumor Immune Estimation Resource 2.0 (TIMER2.0). TIMER2.0 is a sophisticated computational resource specifically designed for assessing the immune landscape within tumors. It enables the examination of how gene expression within tumor cells relates to the composition and activity of immune cells infiltrating the tumor. An essential feature of TIMER2.0 is its incorporation of purity adjustment. This adjustment accounts for the presence of non-immune cells within the tumor samples. By considering the purity of the tumor, the tool enhances the accuracy of the analysis and provides a more precise understanding of the relationship between gene expression and immune cell infiltration.
Moreover, to assess the correlation between the variables of interest, Spearman's correlation test was employed. Spearman's correlation calculates the strength and direction of the association between two variables. A positive correlation is indicated by a Spearman's rho (ρ) value greater than zero (ρ > 0), suggesting that the variables tend to increase or decrease together. Conversely, a negative correlation is characterized by a rho value less than zero (ρ < 0), indicating an inverse relationship between the variables.
Analysis of statistical bioinformatics
In the study, a comprehensive analysis was conducted on the TCGA-COAD cohort to investigate the top mutation trends and gene patterns. Particularly, the focus of the analysis was on the nucleotide variations occurring in the APC and TP53 genes, which are known to play crucial roles in colon tumors.
To evaluate the significance of these genes in the context of colon tumors, a comparison was made between the gene expressions of APC and TP53 in the TCGA-COAD group and the GTEx group, representing healthy colon tissue. This assessment aimed to discern any differential expressions of APC and TP53 mRNA levels between the two groups.
To perform this analysis, a one-way ANOVA test was employed. This statistical test allowed for the examination of variations in gene expressions and provided insights into the potential significance of APC and TP53 in the colon tumors' genome.
Furthermore, the study aimed to determine the prognostic value of the APC and TP53 gene mutations. To achieve this, Kaplan-Meier survival curves were utilized. These curves are widely used in survival analysis to visualize the probability of overtime. By analyzing the survival curves, we were able to assess the impact of APC and TP53 gene mutations on overall survival (OS).
To compare the high- and low-gene mutation profiles in TCGA-COAD patients, a log-rank test was employed. The log-rank test is a statistical method used to determine if there is a significant difference in survival between two or more groups. In this case, it allowed for the evaluation of whether the presence or absence of mutations in the APC and TP53 genes affected the overall survival of patients with colon tumors.
By employing these statistical and bioinformatics techniques, the study aimed to provide valuable insights into the role of APC and TP53 gene mutations in colon tumors, shedding light on potential prognostic markers and contributing to a better understanding of the underlying mechanisms of the disease.
Ethics statement
The samples used in this study were obtained from publicly available databases; therefore, formal ethics approval was not required.
Results
Demographics and gene mutation profiles
The genetic and clinical data of 461 cases were collected by the TCGA-COAD project. The average patient's age was 67.5 ± 14 years.
Overall data about TCGA-COAD patients are summarized in Table 1.
Demographic, clinical, and histological data of TCGA-COAD patients
| Variable | Data Primary site | ||
| Colon | Rectosigmoid junction | ||
| Case no | 454 | 7 | |
| Sex | Female (%) | 214 (47.14) | 2 (28.6) |
| Male (%) | 238 (52.42) | 5 (71.4) | |
| Not report (%) | 2 (0.44) | – | |
| Race | Asian (%) | 11 (2.43) | – |
| Black or African-American (%) | 58 (12.77) | 1 (14.2) | |
| White (%) | 211 (46.5) | 3 (42.9) | |
| Not report (%) | 174 (38.3) | 3 (42.9) | |
| Vital status | Alive (%) | 354 (77.98) | 3 (42.9) |
| Dead (%) | 98 (21.58) | 4 (57.1) | |
| Not report (%) | 2 (0.44) | – | |
| Histological type | Mucinous adenocarcinoma (%) | 59 (12.9) | 1 (14.2) |
| Adenocarcinoma (%) | 382 (84.1) | 6 (85.8) | |
| Pupillary Adenocarcinoma (%) | 2 (0.4) | – | |
| Not report (%) | 12 (2.6) | – | |
| APC Mutation no in colon | 303 (66.74) | ||
| TP53 Mutation no | 6 (85.71) | ||
APC was the most frequent gene by the transcriptome examination in colon sites (66.74%). It was followed by TTN (51.98%), TP53 (50.88%), KRAS (40.31%), MUC16 (31.72%), SYNE1 (30.62%), PIK3CA (27.31%), FAT4 (24.23%), OBSCN (23.79%), ZHFX4 (22.69%), RYR2 (21.37%), USH2A (20.04%), DNAH5 (20.04%), CSMD3 (19.60%), FAT3 (19.60%), LR91B (19.38 %), RYR3 (18.5%), PCLO (18.28%), RYR1 (18.06%), and DST (17.62%) (Fig. 1A). On the other hand, TP53 was the most frequent gene by the transcriptome examination in rectosigmoid junction sites (85.71%). It was followed by APC (57.14%), FAT4 (42.86%), AHNAK2 (42.86%), TTN (42.86%), DDX10 (28.57%), CDH8 (28.57%), OPRK1 (28.57%), BRAF (28.57%), RANBP6 (28.57%), DST (28.57%), CPD (28.57%), TAF4 (28.57%), C8B (28.57%), ANK3 (28.57%), CSMD3 (28.57%), SCN11A (28.57%), NUP205 (28.57%), C2orf16 (28.57%), and PCDHB6 (28.57%) (Fig. 1B).
Distribution of the most frequent mutated genes in the TCGA-COAD project for both primary site (A) colon and (B) rectosigmoid junction
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
Expression profiles and mutations of the top 50 genes in TCGA-COAD are shown in the Oncogrid (Fig. 2).
OncoGrid of top 50 mutated genes with impact mutations on the TCGC-COAD cohort for both primary site (A) colon (200 mutated cases) and (B) rectosigmoid junction (7 mutated cases)
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
Continued
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
From the GTEx dataset, a total of 318 samples of normal colon-sigmoid tissue and 368 sample of normal colon-transverse were included. The differential analysis revealed a higher expression of APC and TP53 mRNA levels in the tumor than in normal tissue (Fig. 3).
Box plots reveal the differential APC and TP53 mRNA expression levels in TCGA-COAD and GTEx datasets
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
Survival analysis
The Kaplan-Meier curves presented in Fig. 4 illustrate the overall survival of patients based on the levels of APC and TP53 gene expression in colon adenocarcinoma and rectosigmoid junction, respectively. The log-rank P-values associated with these curves were calculated to assess the statistical significance of the observed differences in survival.
Kaplan–Meyer curves showing the Overall Survival in TCGA-COAD patients according to the level of (A) APC and (B) TP53 TPM
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
The x-axis represents the duration of survival in years. The y-axis represents the probability of survival. The curve itself consists of a series of steps, each corresponding to a specific time point in the study. These steps indicate the occurrence of patient deaths, and the height of each step illustrates the proportion of patients who were still alive at that particular time point. This visual representation allows for a dynamic understanding of the changing survival rates over time. The log-rank P-value serves as a statistical measure that evaluates whether the survival curves of the compared groups are significantly different. A P-value less than 0.05 is considered statistically significant.
Regarding the high-APC mutation profile in the colon, the Kaplan-Meier curve shows a trend towards a difference in overall survival, although the log-rank P-value (1.66e-1) suggests that this difference is not statistically significant. This finding indicates that while there may be some variation in survival outcomes based on the APC mutation status, it does not reach statistical significance in this particular cohort.
Similarly, for the high-TP53 mutation profile in the rectosigmoid junction, the Kaplan-Meier curve demonstrates a trend towards a difference in overall survival. However, the log-rank P-value (8.15e-2) indicates that this difference is also not statistically significant in the analyzed patient cohort.
Immune landscape in APC and TP53-related colon microenvironment
Spearman's correlation analysis of immune subpopulations applied in the TCGA-COAD cohort revealed a positive correlation between mRNA APC mutation expression (log2 TPM) and infiltrating T cell CD4+ (ρ = 0.393, P = 1.29e-11), T cell CD8+ (ρ = 0.183, P = 2.3e-03), NK cell (ρ = 0.265; P = 8.31e-06), and Macrophage (ρ = 0.302, P = 3.04e-07) (Fig. 5). However, it demonstrated a negative correlation between mRNA TP53 mutation expression and infiltrating NK cell (ρ = −045; P = 4.61e-01), and Macrophage (ρ = −0.038, P = 5.31e-01). Contrarily, T cell CD4+ (ρ = 0.047, P = 4.39e-01), and T cell CD8+ (ρ = 0.131, P = 3e-02) were predominant and positive correlation within the tumor microenvironment (Fig. 6).
Scatter plots picturing the correlation of mRNA APC expression and the immune infiltration of T cell CD4+ (A), T cell CD8+ (B), NK cell (C), and Macrophage (D) in the TCGC-COAD project
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
Scatter plots picturing the correlation of mRNA TP53 expression and the immune infiltration of T cell CD4+ (A), T cell CD8+ (B), NK cell (C), and Macrophage (D) in the TCGC-COAD project
Citation: European Journal of Microbiology and Immunology 14, 2; 10.1556/1886.2024.00015
Discussion
This study focused on investigating the expression profiles of the APC and TP53 genes in colon adenocarcinoma (COAD) and their association with the immune microenvironment. The results revealed that both APC and TP53 mutations were highly prevalent in COAD patients, with APC being the most frequently mutated gene in colon sites and TP53 in rectosigmoid junction sites.
These findings are consistent with previous studies that have also reported frequent mutations in APC and TP53 in COAD [18, 19].
Gene expression patterns play a crucial role in understanding the underlying mechanisms of various biological processes. Mutations in specific genes can significantly impact gene expression patterns and contribute to the development of diseases. In the context of colon cancer, localization of mutations in specific genes can disrupt normal gene expression patterns and contribute to tumor development [20].
APC mutations were found to be predominantly associated with colon sites. Mutations in the APC gene can lead to aberrant gene expression patterns, contributing to tumor formation in the colon. The APC gene is known to play a crucial role in the Wnt signaling pathway, which regulates cell proliferation and differentiation. Mutations in APC lead to dysregulated Wnt signaling and contribute to the initiation and progression of COAD [9, 21, 22]. Similarly, TP53 mutations were more prevalent in rectosigmoid junctions. TP53 is a tumor suppressor gene involved in regulating cell cycle arrest, DNA repair, and apoptosis. Mutations in TP53 disrupt its tumor-suppressive functions, allowing for uncontrolled cell growth and tumor formation [23]. These findings highlight the spatial heterogeneity of gene mutations within the colon region. The distinct prevalence of APC mutations in the colon and TP53 mutations in the rectosigmoid junction suggests potential variations in the molecular pathways underlying colorectal cancer development.
The differential expression analysis demonstrated significantly higher levels of APC and TP53 mRNA in tumor samples compared to normal colon tissue [24–26]. This upregulation of APC and TP53 in COAD is consistent with their known roles as oncogenes in COAD. These findings further support the importance of these genetic alterations in driving tumor development and progression [27, 28].
Further demonstrated a strong correlation between these mutations and a diminished response to immunotherapy, highlighting the importance of considering APC and TP53 mutation status when predicting the efficacy of immunotherapeutic interventions in colon adenocarcinoma patients [29–31]. The association between APC and TP53 mutations and the response to immunotherapy in cancer treatment was determined and observed a strong correlation between the presence of these mutations and a diminished response to immunotherapy in cancer especially in colon adenocarcinoma patients. Particularly, patients with APC and TP53 mutations exhibited lower response rates and shorter progression-free survival compared to patients without these mutations [32–35].
Survival analysis using Kaplan-Meier curves revealed that patients with a high-APC mutation profile in colon and a high-TP53 mutation profile in rectosigmoid junction had worse overall survival outcomes. Thus, while the Kaplan-Meier curves provide valuable insights into the overall survival trends based on APC and TP53 gene expression profiles, the lack of statistical significance suggests that further investigation is needed to fully understand the impact of these genetic alterations on survival outcomes. Future studies with larger sample sizes and comprehensive clinical data are warranted to validate and expand upon these findings.
These results suggest that the presence of APC and TP53 mutations may serve as prognostic markers for COAD patients. Similar associations between APC and TP53 mutations and poor prognosis have been reported in other studies, highlighting the clinical relevance of these genetic alterations [36–38].
The presence of APC mutations was significantly associated with worse survival outcomes in colon cancer. Patients with APC mutations exhibited shorter overall survival and poor response of immunotherapy compared to those without these mutations [33, 39]. Besides, TP53 mutations are significantly associated with adverse clinicopathological features and poor prognosis in COAD patients. Patients with TP53 mutations had a higher likelihood of tumor metastasis, advanced disease stage, and reduced overall survival rates compared to those without TP53 mutations [35, 40]. These findings emphasize the importance of assessing APC and TP53 mutation status as a potential prognostic marker in COAD patients.
In terms of the immune microenvironment, our analysis demonstrated a strong positive correlation between APC mutation expression and the infiltration of T cell CD4+, T cell CD8+, NK cells, and macrophages. This suggests that APC mutations may promote an immune response characterized by increased T cell and NK cell activity, as well as macrophage infiltration. These findings align with previous research indicating that APC mutations can modulate the immune response and influence tumor-infiltrating lymphocytes [41, 42]. Li et al. also reported the strong association between APC and an unfavorable response to immunotherapy in cases of colon cancer [39]. On the other hand, TP53 mutation expression showed a negative correlation with NK cells and macrophages but a positive correlation with T cell CD4+ and T cell CD8+. This suggests that TP53 mutations may have a different impact on the immune microenvironment, potentially leading to immune evasion mechanisms. These results are intriguing and warrant further investigation to elucidate the underlying mechanisms by which TP53 mutations affect immune cell infiltration and function.
Comparing our findings with other studies, several research articles have reported similar associations between APC and TP53 mutations and poor prognosis in COAD patients. Furthermore, studies have also highlighted the role of the immune microenvironment in colon cancer, with tumor-infiltrating lymphocytes and macrophages being implicated in tumor progression and response to therapy [43, 44].
In addition to gene mutations, recent studies have shed light on the role of the immune microenvironment in colon cancer. The immune system plays an important function in recognizing and eliminating cancer cells. Tumor-infiltrating lymphocytes and macrophages are key components of the immune response within the tumor microenvironment. Tumor-infiltrating lymphocytes are immune cells that infiltrate the tumor and can exhibit anti-tumor activity, while macrophages can have both pro- and anti-tumor functions depending on their polarization state [45, 46]. Emerging evidence suggests that the composition and activity of Tumor-infiltrating lymphocytes and macrophages in the tumor microenvironment can influence tumor progression and response to therapy. High levels of Tumor-infiltrating lymphocytes, particularly cytotoxic T lymphocytes, have been associated with improved survival and better response to immunotherapy in colorectal cancer patients. Conversely, an abundance of tumor-associated macrophages with an immunosuppressive phenotype has been linked to poor prognosis and resistance to treatment [47].
However, it is important to note that there are some discrepancies in the literature regarding the precise relationship between APC, TP53 mutations, and the immune microenvironment in COAD. Some studies have reported conflicting results, showing different immune cell profiles associated with APC and TP53 mutations. These discrepancies may be attributed to variations in patient cohorts, sample sizes, and methodologies employed across different studies [48, 49].
In addition, our study focused specifically on the correlation between APC and TP53 mutations and immune cell infiltration, but other genetic alterations and molecular pathways may also influence the immune landscape in COAD. Future studies should consider integrating multi-omics data to comprehensively analyze the interplay between genetic alterations, immune cells, and other components of the tumor microenvironment.
The findings regarding the impact of APC and TP53 mutations on immunotherapy response have important implications for the future of immunotherapeutic approaches, particularly in patients with Microsatellite instability (MSI)-high tumors. Currently, immunotherapy is effective for only a subset of patients, and there is a need to expand the patient population that can benefit from these treatments. The identification of specific genetic alterations, such as APC and TP53 mutations, that influence immunotherapy response provides an opportunity for developing strategies to enhance the effectiveness of immunotherapeutic interventions. By integrating these genetic insights into treatment planning, researchers and clinicians can potentially refine and optimize immunotherapeutic approaches for a broader range of patients. One potential avenue for enhancing immunotherapeutic strategies is through combination therapies. Combining immune checkpoint inhibitors with targeted therapies or other immunomodulatory agents could overcome resistance mechanisms associated with APC and TP53 mutations. By targeting both genetic alterations and the immune microenvironment, these combination approaches may improve treatment response rates and increase the percentage of patients who derive clinical benefit from immunotherapy [50, 51].
In conclusion, our study provides valuable insights into the expression profiles of APC and TP53 genes in COAD and their association with the immune microenvironment. The high prevalence of APC and TP53 mutations in COAD, along with their correlation with immune cell infiltration, highlights their potential as prognostic markers and therapeutic targets. Further research is necessary to validate these findings and uncover the underlying mechanisms driving the relationship between genetic alterations, immune response, and clinical outcomes in COAD. These findings suggest that APC and TP53 gene mutations are not only associated with poor prognosis and shorter survival but also influence the composition of immune cells within the colon microenvironment. The infiltration of T cells (CD4+ and CD8+), NK cells, and macrophages appears to play a crucial role in tumor advancement, immune evasion, and response to standard chemotherapy. Overall, our study contributes to the growing body of knowledge in the field of colon adenocarcinoma and underscores the importance of considering the genetic and immunological aspects of the disease. By elucidating the relationship between gene mutations, immune cell infiltration, and clinical outcomes, we move closer to a more personalized and targeted approach to the management of COAD.
Limitations
One of the limitations of this study is the relatively small sample size, particularly in the rectosigmoidal group, which consisted of only seven patients. While this sample size provided preliminary insights into the expression profiles of APC and TP53 genes in colon adenocarcinoma, it may limit the generalizability of the findings. Larger-scale studies involving a more diverse patient population are needed to validate and extend these results. Furthermore, the interpretation of our findings should consider that patient cohorts across different studies may exhibit variations in demographics, clinical characteristics, and treatment regimens. These factors may influence the gene expression patterns and immune microenvironment, potentially leading to discrepancies in results. Therefore, caution should be exercised when comparing our findings with those from other studies. Also, while we have focused on the association between APC and TP53 mutations and the immune microenvironment, it is important to acknowledge that other genetic alterations and molecular pathways can also influence the immune landscape in colon adenocarcinoma. The interplay between these factors may contribute to the complexity of the immune response observed in our study. Future research should consider integrating multi-omics data to comprehensively analyze the interactions between genetic alterations, immune cells, and other components of the tumor microenvironment. It should be noted, our study primarily focused on the expression profiles of APC and TP53 genes and their correlation with immune cell infiltration. However, it is important to note that functional analysis, such as protein expression and activity assays, was not conducted in this study. Further investigations are necessary to elucidate the functional consequences of APC and TP53 mutations on the immune response in colon adenocarcinoma. Although efforts were made to minimize bias during data collection and analysis, it is important to acknowledge that inherent biases may exist in retrospective studies. These biases include selection bias, information bias, and confounding variables that may influence the accuracy and interpretation of the results. Additionally, further investigations involving in vivo studies or preclinical models would serve to expand upon and validate the findings obtained from this study.
Despite these limitations, our study contributes to the understanding of the expression patterns of APC and TP53 genes in colon adenocarcinoma and their association with the immune microenvironment. By acknowledging these limitations, future research can build upon these findings to provide a more comprehensive understanding of the genetic and immunological factors influencing colon adenocarcinoma progression and treatment response.
Conflict of interest
There is no conflict of interest.
Authors' contributions
AZT, SV wrote the manuscript comprehensively in all parts, and AAS supervised and edited the manuscript scientifically and technically. All the authors read the manuscript comprehensively and confirmed the final revised version. Importantly, there is no conflict of interest.
Funding
There is no funding.
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