# Correlation betweenLRP1B Mutations and Tumor Mutation Burden in Gastric Cancer

Authors: Sizhe Hu; Xiaokang Zhao; Feng Qian; Cancan Jin; Kaishun Hou
Journal: Computational and Mathematical Methods in Medicine
 (2021)

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## Abstract

Background. It has been shown that low-density lipoprotein receptor-related protein 1B (LRP1B) mutations correlate with tumor mutation burden (TMB) and prognosis in patients with melanoma and non-small-cell lung cancer, while the relationship between LRP1B mutations and TMB in gastric cancer needs further study. This study is aimed at exploring the relationship between LRP1B mutations and TMB in gastric cancer. Methods. Mutation frequency profiles of the genes in patients with gastric cancer in TCGA-STAD dataset were analyzed by bioinformatics analysis. The relationship among LRP1B mutations, TMB, and patient clinical features in gastric cancer was investigated by the chi-square test. The TMB prediction capacity based on LRP1B mutation status was evaluated by ROC curves. Results. LRP1B is one of the top 10 genes with high gene mutation frequency in gastric cancer. The mutation status of LRP1B in gastric cancer patients was significantly correlated with age and TP53 and MUC16 mutation status. The result of ROC curve analysis revealed that the mutation status of LRP1B could be considered as an indicator of the degree of TMB in patients with gastric cancer. Conclusion. This study presented the relationship between TMB and LRP1B mutations in gastric cancer, providing a novel perspective for gastric cancer prognosis and therapy.


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## Body

## 1. Introduction

Gastric cancer is the fourth most common cancer in the world and the second primary cause of cancer-related deaths, accounting for 6.8% of all new cancer cases worldwide. Additionally, gastric cancer patients commonly show poor prognosis status. As reported, only 5% of gastric cancer patients survived for five years or more after prognosis, and the mortality rate accounts for 10% of all cancers [1]. In China, there were 679,100 new gastric cancer cases and 498,000 death cases in 2015, reaching more than half of global gastric cancer deaths [2].In recent years, immune checkpoint blockade (ICB) therapies, including anti-tumor antibody-4 and/or anti-pd-1, have shown durable antitumor effects in the treatment of cancers [3–5]. Tumor mutation burden (TMB), defined as the total number of mutations (nonsynonymous mutation) detected per million bases in the DNA of tumor cells, is widely referred to as a biomarker correlative with clinical responses to ICB in the treatment of melanoma [6–8], non-small-cell lung cancer [9, 10], colorectal cancer, and gastric cancer [11]. TMB detection is based on extensive next-generation sequencing (NGS) or whole-exome sequencing. Recently, several studies have reported that some simple methods such as single gene mutation detection can be used to predict TMB [12]. Numerous studies have shown that mutations in genomic integrity-related genes such as TP53 [13] and ATR [14] may lead to genomic instability and thus contribute to a high genomic mutation rate. Besides, mutations of these genes have been reported to be related to TMB [6, 9, 15]. Therefore, studying the correlation between the mutations of key genes and TMB in gastric cancer is conducive to the guidance of immunotherapy on gastric cancer patients.Low-density lipoprotein receptor-related protein 1B (LRP1B) is a recognized tumor suppressor gene that encodes an endocytosed ldl receptor. LRP1B expression is reduced in many cancers, and it is a common mutant gene in human cancers [15–17]. Among the studies on LRP1B, it was found that LRP1B plays an important role and may serve as a prognostic marker for cancer during the development of various cancers including gastric cancer [18, 19]. In addition, the significant associations between LRP1B mutations and TMB in lung cancer and melanoma have also been reported [15, 20]. However, there are few studies about the correlation between LRP1B mutation and TMB in gastric cancer.Here, we explored the mutation status ofLRP1B in gastric cancer by analyzing TCGA-STAD dataset. The correlation between clinical features of patients with gastric cancer and LRP1B was analyzed. And it was assessed whether the mutation status of LRP1B could be the predictor for the TMB level in patients with gastric cancer. The findings above were supposed to be useful for guidance of immunotherapy for cancer patients.


## 2. Materials and Methods

### 2.1. Data Downloading

The masked somatic mutation data of gastric cancer samples and the corresponding clinical data were downloaded from TCGA database. Using Mmutect2 software [21], the mutation data of 441 samples was extracted. Then, 372 samples with complete clinical information were retained for later analysis.


### 2.2. Statistical Analysis of Mutation Information

R packagesMaftools [22] and GenVisR [23] were used to analyze the frequency and mutation type of mutant genes in gastric cancer and visualize the analysis results in the form of histogram and waterfall diagrams. Differences in the distribution of LRP1B mutant-type versus wild-type samples among different clinical characteristics (gender, age, survival status, grade, stage, T, N, M, KRAS mutation, TP53 mutation, and MUC16 mutation) were analyzed by the chi-square test. P<0.05 was considered statistically significant.


### 2.3. Correlation Analysis of LRP1B Mutations and TMB

According to the definition of TMB, the TMB values of 372 gastric cancer samples in TCGA were calculated, and the gastric cancer samples were divided into high-TMB and low-TMB groups taking the median value as the threshold. Kaplan-Meier survival analysis was performed for the high- and low-TMB groups using the R package survival. The analysis results were tested by the log-rank test, andP<0.05 was considered statistically significant.The distribution of samples with differentKRAS, TP53, MUC16, and LRP1B mutation statuses in the high- and low-TMB groups was analyzed by the chi-square test, and P<0.05 was considered to indicate a significant difference in distribution. To assess the accuracy of LRP1B mutation status in predicting the high and low level of TMB, the area under the curve (AUC) was analyzed and calculated by the ROC curve.


## 2.1. Data Downloading

The masked somatic mutation data of gastric cancer samples and the corresponding clinical data were downloaded from TCGA database. Using Mmutect2 software [21], the mutation data of 441 samples was extracted. Then, 372 samples with complete clinical information were retained for later analysis.


## 2.2. Statistical Analysis of Mutation Information

R packagesMaftools [22] and GenVisR [23] were used to analyze the frequency and mutation type of mutant genes in gastric cancer and visualize the analysis results in the form of histogram and waterfall diagrams. Differences in the distribution of LRP1B mutant-type versus wild-type samples among different clinical characteristics (gender, age, survival status, grade, stage, T, N, M, KRAS mutation, TP53 mutation, and MUC16 mutation) were analyzed by the chi-square test. P<0.05 was considered statistically significant.


## 2.3. Correlation Analysis of LRP1B Mutations and TMB

According to the definition of TMB, the TMB values of 372 gastric cancer samples in TCGA were calculated, and the gastric cancer samples were divided into high-TMB and low-TMB groups taking the median value as the threshold. Kaplan-Meier survival analysis was performed for the high- and low-TMB groups using the R package survival. The analysis results were tested by the log-rank test, andP<0.05 was considered statistically significant.The distribution of samples with differentKRAS, TP53, MUC16, and LRP1B mutation statuses in the high- and low-TMB groups was analyzed by the chi-square test, and P<0.05 was considered to indicate a significant difference in distribution. To assess the accuracy of LRP1B mutation status in predicting the high and low level of TMB, the area under the curve (AUC) was analyzed and calculated by the ROC curve.


## 3. Results

### 3.1. The Mutation Status ofLRP1B in the Gastric Cancer Genome

The top 20 genes with mutation frequency were visualized by analyzing mutation data from 372 gastric cancer patients in TCGA-STAD dataset (Figure1). LRP1B with the 7th highest mutation frequency among 20 genes performed a relatively higher mutation frequency (0.176). To investigate the role of LRP1B mutations in gastric cancer, we analyzed the connection between LRP1B mutations and several important clinicopathological features as well as some important biomarker genes in gastric cancer patients. The results showed a significant difference (P<0.05) in the mutation status of LRP1B between patients≥60 years old and <60 years old. Besides, it was also shown that LRP1B mutations were significantly correlated with mutations in TP53 and MUC16 (Table 1). Based on the above analysis results, the frequency of LRP1B mutation was high in patients with gastric cancer, and distribution of LRP1B mutation was significantly different in patients among different age periods and with different TP53 and MUC16 mutation statuses.Figure 1
Mutation frequencies of different genes in TCGA-STAD dataset. The top plate represents the probability of synonymous and nonsynonymous mutations per million bases in gastric cancer patients in the dataset, the plate on the far left shows the top 20 genes with mutation frequency in this dataset, the middle plate shows the mutation types of top 20 high-frequency mutation genes in gastric cancer samples, and the plate on the bottom shows the clinical information (stage, gender) of gastric cancer samples. Only information on the 318 mutant samples with top 20 genes with mutation frequency.Table 1
Relationship betweenLRP1B gene mutation status and clinical characteristics in patients with gastric cancer.
LRP1B MUT (n=112)LRP1B WT (n=260)P valueGenderFemale36 (32.1%)104 (40.0%)0.187Male76 (67.9%)156 (60.0%)Age (years)Age<6025 (22.3%)91 (35.0%)0.021Age≥6087 (77.7%)169 (65.0%)EventYes39 (34.8%)90 (34.6%)1No73 (65.2%)170 (65.4%)GradeG11 (0.9%)7 (2.7%)0.462G236 (32.1%)90 (34.6%)G375 (67.0%)163 (62.7%)StageStage I14 (12.5%)31 (11.9%)0.883Stage II34 (30.4%)86 (33.1%)Stage III50 (44.6%)117 (45.0%)Stage IV14 (12.5%)26 (10.0%)TT17 (6.2%)10 (3.8%)0.389T217 (15.2%)56 (21.5%)T354 (48.2%)125 (48.1%)T434 (30.4%)69 (26.5%)NN039 (34.8%)78 (30.0%)0.565N126 (23.2%)73 (28.1%)N221 (18.8%)57 (21.9%)N326 (23.2%)52 (20.0%)MM0103 (92.0%)242 (93.1%)0.872M19 (8.0%)18 (6.9%)KRASMut10 (8.9%)22 (8.5%)1Wild102 (91.1%)238 (91.5%)TP53Mut62 (55.4%)112 (43.1%)0.039Wild50 (44.6%)148 (56.9%)MUC16Mut67 (59.8%)73 (28.1%)<0.001Wild45 (40.2%)187 (71.9%)


### 3.2.LRP1B Mutations Are Associated with TMB

To explore the effects of TMB on gastric cancer prognosis, survival analysis was conducted on the high- and low-TMB groups based on TCGA-STAD dataset, and the results showed a significant difference at the prognosis between the high- and low-TMB groups, where the high-TMB group showed relatively optimal survival status (Figure2). LRP1B mutations have been reported to be significantly associated with TMB [15, 24]. We analyzed the relationship between LPR1B, KRAS, TP53, and MUC16 mutations and TMB by statistical analysis. The results showed that there were significant differences in the distribution of mutation status of LPR1B, KRAS, TP53, and MUC16 genes in patients with gastric cancer in the high- and low-TMB groups (Table 2). Mutations in KRAS, TP53, and MUC16 have been proven to play an important role in the prognosis of gastric cancer and are closely related to TMB. Based on the above, we concluded that there is a significant correlation between LRP1B and TMB.Figure 2
Survival analysis of high- and low-TMB groups in TCGA-STAD dataset.Table 2
Correlation between gene mutation and TMB.
Low TMB (n=186)High TMB (n=186)P valueKRASMut7 (3.8%)25 (13.4%)0.001Wild179 (96.2%)161 (86.6%)TP53Mut75 (40.3%)99 (53.2%)0.016Wild111 (59.7%)87 (46.8%)LRP1BMut32 (17.2%)80 (43.0%)<0.001Wild154 (82.8%)106 (57.0%)MUC16Mut36 (19.4%)104 (55.9%)<0.001Wild150 (80.6%)82 (44.1%)


### 3.3. The Predictive Value of the Mutation ofLRP1B to TMB Value in Gastric Cancer

To further explore whetherLRP1B mutations could effectively predict the TMB level in gastric cancer patients, the ROC curve was plotted on LRP1B expression based on TCGA-STAD database. The result demonstrated that the AUC value was 0.602 with 95% confidence interval of 0.550-0.655, which indicated that the level of TMB could be predicted effectively by the LRP1B mutation status of gastric cancer patients (Figure 3). The above results indicated that LRP1B mutation had a certain predictive effect on the level of TMB, which may provide new ideas for later targeted therapy and immunotherapy of gastric cancer.Figure 3
Predictive value ofLRP1B mutations to the level of TMB in gastric cancer patients from TCGA-STAD dataset.


## 3.1. The Mutation Status ofLRP1B in the Gastric Cancer Genome

The top 20 genes with mutation frequency were visualized by analyzing mutation data from 372 gastric cancer patients in TCGA-STAD dataset (Figure1). LRP1B with the 7th highest mutation frequency among 20 genes performed a relatively higher mutation frequency (0.176). To investigate the role of LRP1B mutations in gastric cancer, we analyzed the connection between LRP1B mutations and several important clinicopathological features as well as some important biomarker genes in gastric cancer patients. The results showed a significant difference (P<0.05) in the mutation status of LRP1B between patients≥60 years old and <60 years old. Besides, it was also shown that LRP1B mutations were significantly correlated with mutations in TP53 and MUC16 (Table 1). Based on the above analysis results, the frequency of LRP1B mutation was high in patients with gastric cancer, and distribution of LRP1B mutation was significantly different in patients among different age periods and with different TP53 and MUC16 mutation statuses.Figure 1
Mutation frequencies of different genes in TCGA-STAD dataset. The top plate represents the probability of synonymous and nonsynonymous mutations per million bases in gastric cancer patients in the dataset, the plate on the far left shows the top 20 genes with mutation frequency in this dataset, the middle plate shows the mutation types of top 20 high-frequency mutation genes in gastric cancer samples, and the plate on the bottom shows the clinical information (stage, gender) of gastric cancer samples. Only information on the 318 mutant samples with top 20 genes with mutation frequency.Table 1
Relationship betweenLRP1B gene mutation status and clinical characteristics in patients with gastric cancer.
LRP1B MUT (n=112)LRP1B WT (n=260)P valueGenderFemale36 (32.1%)104 (40.0%)0.187Male76 (67.9%)156 (60.0%)Age (years)Age<6025 (22.3%)91 (35.0%)0.021Age≥6087 (77.7%)169 (65.0%)EventYes39 (34.8%)90 (34.6%)1No73 (65.2%)170 (65.4%)GradeG11 (0.9%)7 (2.7%)0.462G236 (32.1%)90 (34.6%)G375 (67.0%)163 (62.7%)StageStage I14 (12.5%)31 (11.9%)0.883Stage II34 (30.4%)86 (33.1%)Stage III50 (44.6%)117 (45.0%)Stage IV14 (12.5%)26 (10.0%)TT17 (6.2%)10 (3.8%)0.389T217 (15.2%)56 (21.5%)T354 (48.2%)125 (48.1%)T434 (30.4%)69 (26.5%)NN039 (34.8%)78 (30.0%)0.565N126 (23.2%)73 (28.1%)N221 (18.8%)57 (21.9%)N326 (23.2%)52 (20.0%)MM0103 (92.0%)242 (93.1%)0.872M19 (8.0%)18 (6.9%)KRASMut10 (8.9%)22 (8.5%)1Wild102 (91.1%)238 (91.5%)TP53Mut62 (55.4%)112 (43.1%)0.039Wild50 (44.6%)148 (56.9%)MUC16Mut67 (59.8%)73 (28.1%)<0.001Wild45 (40.2%)187 (71.9%)


## 3.2.LRP1B Mutations Are Associated with TMB

To explore the effects of TMB on gastric cancer prognosis, survival analysis was conducted on the high- and low-TMB groups based on TCGA-STAD dataset, and the results showed a significant difference at the prognosis between the high- and low-TMB groups, where the high-TMB group showed relatively optimal survival status (Figure2). LRP1B mutations have been reported to be significantly associated with TMB [15, 24]. We analyzed the relationship between LPR1B, KRAS, TP53, and MUC16 mutations and TMB by statistical analysis. The results showed that there were significant differences in the distribution of mutation status of LPR1B, KRAS, TP53, and MUC16 genes in patients with gastric cancer in the high- and low-TMB groups (Table 2). Mutations in KRAS, TP53, and MUC16 have been proven to play an important role in the prognosis of gastric cancer and are closely related to TMB. Based on the above, we concluded that there is a significant correlation between LRP1B and TMB.Figure 2
Survival analysis of high- and low-TMB groups in TCGA-STAD dataset.Table 2
Correlation between gene mutation and TMB.
Low TMB (n=186)High TMB (n=186)P valueKRASMut7 (3.8%)25 (13.4%)0.001Wild179 (96.2%)161 (86.6%)TP53Mut75 (40.3%)99 (53.2%)0.016Wild111 (59.7%)87 (46.8%)LRP1BMut32 (17.2%)80 (43.0%)<0.001Wild154 (82.8%)106 (57.0%)MUC16Mut36 (19.4%)104 (55.9%)<0.001Wild150 (80.6%)82 (44.1%)


## 3.3. The Predictive Value of the Mutation ofLRP1B to TMB Value in Gastric Cancer

To further explore whetherLRP1B mutations could effectively predict the TMB level in gastric cancer patients, the ROC curve was plotted on LRP1B expression based on TCGA-STAD database. The result demonstrated that the AUC value was 0.602 with 95% confidence interval of 0.550-0.655, which indicated that the level of TMB could be predicted effectively by the LRP1B mutation status of gastric cancer patients (Figure 3). The above results indicated that LRP1B mutation had a certain predictive effect on the level of TMB, which may provide new ideas for later targeted therapy and immunotherapy of gastric cancer.Figure 3
Predictive value ofLRP1B mutations to the level of TMB in gastric cancer patients from TCGA-STAD dataset.


## 4. Discussion

In this study, we found thatLRP1B is one of the top 20 genes with mutation frequency in gastric cancer through the analysis of mutation data from gastric cancer patients in TCGA-STAD dataset. In the correlation analysis of LRP1B mutation and clinical features of gastric cancer patients, it was found that the mutation of LRP1B was significantly correlated with age, TP53 mutation, and MUC16 mutation. TP53 is the most common somatic mutation in human cancers, and tumors with TP53 mutations in breast cancer often perform higher invasive and metastatic potential [25]. It has been reported that the mutation frequency of TP53 was significantly higher in patients with liver metastasis of gastric cancer than in gastric cancer patients without liver metastasis [26]. MUC16 encodes cancer antigen 125, a commonly mutated gene in gastric cancer, and its mutation is associated with higher TMB [27]. Our results therefore imply that LRP1B mutations in gastric cancer may indicate TMB mutations and are closely related to the progression of gastric cancer.TMB is a novel predictive biomarker with a good response to immunotherapy and a quantitative measure approach to quantify the total number of somatic nonsynonymous mutations per megabit of the genome in cancer cell DNA [28]. Zhou et al. [29] studied the effect of KIAA1211 mutations and TMB on the prognosis of non-small-cell lung cancer patients and performed survival analysis, demonstrating that both TMB level and high expression of KIAA1211 are related to a good prognostic factor for non-small-cell lung cancer, and similarly, KIAA1211 mutant frequency is positively correlated with TMB level. In this study, the relationship between LRP1B mutations and TMB in gastric cancer patients from TCGA database was analyzed, and it was found that LRP1B mutations were significantly associated with TMB. In addition, we found that the LRP1B mutation in gastric cancer patients in TCGA-STAD dataset could predict the level of TMB in patients to some extent by ROC curve analysis. In a previous study, Chen et al. [30] found that significant mutations of LRP1B in melanoma and non-small-cell lung cancer were associated with their prognosis and that patients with LRP1B mutations had higher level of TMB and better immunotherapeutic efficacy. Although this paper analyzed and discussed the correlation between LRP1B and TMB in melanoma and non-small-cell cancer, the major conclusion is consistent with our research. In summary, LRP1B mutations can indicate the degree of TMB in gastric cancer. In conclusion, LRP1B could be used as a potential biomarker in patients with gastric cancer.This study found thatLRP1B was mutated more frequently in gastric cancer and was significantly correlated with TMB. This finding may provide new ideas for the role of LRP1B mutations in the prognosis and treatment of gastric cancer. Although this research has a preliminary study on the relationship between LRP1B and TMB and achieved some progress, it needs further research. Therefore, the role of LRP1B mutations and TMB in the prognosis after immunotherapy in gastric cancer patients can be further explored in subsequent studies. Survival analysis and other experiments can be used to explore the effect of LRP1B and TMB on the overall survival and progression-free survival of gastric cancer patients. In conclusion, this study provides new ideas for the subsequent treatment of gastric cancer and also lays a foundation for subsequent in-depth studies.



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