Low expression of KLRB1 predicts poor survival outcomes and is associated with immune infiltration in breast cancer
Original Article

Low expression of KLRB1 predicts poor survival outcomes and is associated with immune infiltration in breast cancer

Xiao Liu1, Qianqian Cui1,2, Nan Qin1

1Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China; 2Department of Breast Surgery, Altaira Nursing Service, Campbelltown, SA, Australia

Contributions: (I) Conception and design: Q Cui, X Liu; (II) Administrative support: N Qin; (III) Provision of study materials or patients: X Liu; (IV) Collection and assembly of data: X Liu; (V) Data analysis and interpretation: Q Cui; (VI) Manuscript writing: X Liu; (VII) Final approval of manuscript: All authors.

Correspondence to: Nan Qin, MN. Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No. 44 Xiaohuayuan Road, Dadong District, Shenyang 110042, China. Email: qn84623@163.com.

Background: KLRB1 is downregulated in various cancer types. Nevertheless, the specific involvement of KLRB1 in the context of breast cancer (BRCA) has not been fully elucidated. This research aimed to explore its clinical value in BRCA.

Methods: A dataset comprising 1,109 BRCA samples and 113 healthy samples was retrieved from The Cancer Genome Atlas (TCGA) database to establish the association between KLRB1 expression and pan-cancer. Subsequently, an analysis was executed to explore the link between KLRB1 and BRCA. T-tests and Chi-squared tests were conducted to assess the expression of KLRB1 and its clinical implications in BRCA. The prognosis-predictive value of KLRB1 in BRCA was assessed using the Kaplan–Meier method and Cox regression analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses screened biological pathways to analyze the association between the immune infiltration level and KLRB1 expression in BRCA. Lastly, the conclusion was validated through quantitative polymerase chain reaction (qPCR), immunohistochemistry (IHC), and Cell Counting Kit-8 (CCK8) assays.

Results: KLRB1 exhibited low expression in patients with BRCA. Furthermore, KLRB1 demonstrated strong diagnostic potential, as indicated by an area under curve (AUC) of 0.712. Kaplan-Meier survival and Cox regression analyses indicated that attenuated expression of KLRB1 was independently linked to unfavorable clinical outcomes. GO and KEGG enrichment analyses were performed on the top 10 genes that exhibited positive and negative correlations with KLRB1. Analysis of genes positively correlated with KLRB1 revealed associations with signaling receptor activator activity, lymphocyte proliferation, mononuclear cell proliferation, leukocyte proliferation, receptor-ligand activity, immunoglobulin binding, and hematopoietic cell lineage signaling pathway. KLRB1 expression exhibited significant correlations with all immune cells. Furthermore, qPCR and IHC outcomes demonstrated that KLRB1 was significantly downregulated in BRCA tissues. CCK8 findings showed a decrease in the proliferation of BRCA MCF7 cells upon knockout of KLRB1.

Conclusions: This research investigated the mechanism and potential therapeutic target of the KLRB1 gene in BRCA. By analyzing the expression and function of the KLRB1 gene, the study aims to find its significant role in the onset and progression of BRCA. This research endeavors to offer novel strategies and approaches for treating BRCA.

Keywords: KLRB1; immune; breast cancer (BRCA); prognosis


Submitted Jul 14, 2023. Accepted for publication Feb 08, 2024. Published online Mar 25, 2024.

doi: 10.21037/tcr-23-1231


Highlight box

Key findings

• KLRB1 is a potential predictive tumor marker for breast cancer (BRCA) patients.

What is known and what is new?

• BRCA seriously endangers women’s health. It is the most commonly diagnosed cancer in women, and ranks second among the causes of cancer-related deaths in women.

• The high expression of KLRB1 is associated with prognostic significance.

What is the implication, and what should change now?

• By analyzing the expression and function of KLRB1 gene, we expect to find its important role in the occurrence and development of BRCA, and provide new strategies and methods for the treatment of BRCA.

• Report about implications and actions is needed.


Introduction

Globally, the burden of breast cancer (BRCA) is increasing. This disease stands as the most prevalent type of cancer in females and a leading contributor to cancer-related mortality (1,2). While advancements in early diagnosis and comprehensive treatment approaches have led to improved prognoses for individuals with BRCA, the 5-year overall survival (OS) rate remains below 20% when metastasis is present (3,4). Hence, there is an urgent need to identify biological markers associated with BRCA prognosis.

Recent research has indicated a potential close association between the KLRB1 gene and the onset and progression of BRCA (5). KLRB1 gene is a cell surface molecule belonging to the C-type lectin family and has a variety of biological functions (6). In the immune response, the KLRB1 gene can inhibit the activation of T lymphocytes, thus playing an immunomodulatory role (7). Multiple investigations have explored the expression and role of the KLRB1 gene in BRCA. These studies have frequently revealed a reduced expression or deletion of the KLRB1 gene within BRCA cells, showcasing a strong association with the invasive and metastatic tendencies of tumors (8,9). Additionally, the KLRB1 gene can affect the biological behavior of BRCA cells by regulating cell apoptosis, cell cycle, cell invasion, and other processes (10). In addition, recent research also found that the KLRB1 gene may be associated with chemotherapy resistance of BRCA, offering a novel potential target for BRCA treatment (11). However, the role of the KLRB1 gene in BRCA remains uncertain. Therefore, this study aims to explore the mechanism and potential therapeutic targets of the KLRB1 gene in BRCA.

As high-throughput sequencing technology has advanced, the generation of extensive omics data has become feasible (12,13,14). The The Cancer Genome Atlas (TCGA)-BRCA gene can help elucidate the causes and prognosis of cancer. This research analyzed the transcriptional levels and prognosis-predictive value of KLRB1 using the data acquired from TCGA-BRCA. Furthermore, the biological mechanism of KLRB1 was investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and the relationship between KLRB1 and immune infiltration levels was assessed. Additionally, quantitative polymerase chain reaction (qPCR), immunohistochemistry (IHC), and Cell Counting Kit-8 (CCK8) experiments provided validation for our findings. We present this article in accordance with the TRIPOD reporting checklist (available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1231/rc).


Methods

Data processing

Expression profiles of 1,109 BRCA tissues and 113 adjoining tissues were retrieved from TCGA. Subsequently, clinicopathological features and predictive data of the individuals were subjected to further screening. RNA-seq (RNA sequencing) data in transcripts per kilobase million (TPM) format from TCGA were uniformly processed. The expression of KLRB1 was evaluated using TCGA. To assess the level of KLRB1 expression in the pan-cancer, extracted data from UCSC Xena were assessed (https://xenabrowser.net/datapages/).

Patients and tissues

Ten pairs of BRCA samples and their matched non-tumor tissues were acquired from Liaoning Cancer Hospital. Every participant provided written informed consent. The approval for this research was granted by the ethics committee of Liaoning Cancer Hospital (20210621) and the study was conducted in accordance with the Declaration of Helsinki (as revised in 2013). The BRCA tissues were collected post-surgery, immediately frozen in liquid nitrogen, and then preserved at −80 ℃ for qPCR analysis.

Gene enrichment analysis

By utilizing the transcriptional sequence from TCGA, the study employed GO and KEGG analyses to determine the genes and pathways associated with KLRB1. The expression data were classified into groups with high and low KLRB1 expression (R “clusterProfiler”).

Immune cell infiltration

To evaluate the relative abundance of infiltrating immune cells in tumor tissues, single sample gene set enrichment analysis (ssGSEA) was conducted. The infiltration levels of immune cells in BRCA expression data were assessed utilizing R “gsva” and an immune data set, including 24 immune cells.

Survival and prognosis analysis

The “survival” graph of KLRB1 was utilized to derive the OS. A division threshold of 50% was chosen as a critical value to divide the cohort into high- and low-expression groups. To examine the prognostic significance of KLRB1 in individuals with BRCA, the “roc” function from the R package was employed for analysis, and visualization was performed using the “ggplot2” package.

Cell culture and transfection

The MCF10A cell line, MCF7 cell line and MDAMB231 cell line was acquired from the Chinese Academy of Sciences and cultured in minimum essential medium (MEM) comprising 10% fetal bovine serum (FBS; GIBCO, Waltham, MA, USA) and 1% penicillin-streptomycin. Cells were cultured in a humidified incubator under 5% CO2 at 37 ℃. One day prior to transfection, MCF7 and MDAMB231 cells were cultured in six-well plates to achieve 50–60% confluence. Transfection of the KLRB1-targeted pEZ-M03 vector was carried out using Lipofectamine 2000 (Thermo Fisher Scientific, Waltham, MA, USA) as per the provided guidelines.

RNA isolation and qPCR analysis

The extraction of tissue RNA was carried out using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Subsequently, the extracted RNA was converted into complementary DNA (cDNA) using the QuantiTect Reverse Transcription Kit (Qiagen, Valencia, CA, USA). The qPCR technique quantifies DNA during each cycle of the PCR reaction through real-time fluorescence measurements. The analyses were conducted using SYBR-Green (Takara, Otsu, Shiga, Japan) as the detection dye, with GAPDH serving as the internal control. The primers employed were as follows: KLRB1 forward primer, 5'-AATTTGCCCTGAAACTTAGCTG-3'; reverse, 5'-GGATGTCACTGAAACACTCAAC-3'. GAPDH forward primer, 5'-GTCTCCTCTGACTTCAACAGCG-3'; reverse, 5'-ACCACCCTGTTGCTGTAGCCAA-3'. The qPCR value was calculated using the 2-delta delta Ct method. We set the Ct value to 15-35, and Ct values not in this range will be excluded.

IHC

IHC was performed using a two-step method according to the manufacturer’s instructions (PV-9000; ZSGB-BIO, Beijing, China). BRCA samples were fixed in 10% formalin, paraffin-embedded, and sectioned into 5-µm slices. The samples were de-waxed with ethanol and blocked to inactivate the endogenous peroxidase activity. Subsequently, antigen retrieval was achieved by heating the samples in a microwave, followed by cooling to room temperature. Blocking was performed using goat serum for 30 minutes at 37 ℃. The samples were then incubated overnight at 4 ℃ with rabbit anti-KLRB1 (Thermo Fisher Scientific 17-5941-82) (1:200). Afterward, incubation with horseradish peroxidase-coupled goat anti-rabbit secondary antibody (PV-9000; ZSGB-BIO, Beijing, China) was conducted at 37 ℃ for 30 minutes. The samples were then stained with 3,3'-diaminobenzidine (DAB). Cell nuclei were stained blue with hematoxylin. The sections were then dehydrated, cleared with xylene, and mounted. KLRB1 expressions were determined by IHC using the streptavidin peroxidase method, with adjacent tissues serving as the controls. The experimental procedure was performed as per the manufacturer’s instructions. Image-Pro Plus 6.0 Software (Media Cybernetics, USA) was used to analyze protein expression and perform statistical analysis of the results obtained by IHC.

Cell colony formation assay

The cells were planted at a density of 1×103/mL in each well of the 6-well plates, with 2 mL of MEM medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. Single-cell-derived clones were allowed to grow for ten days. Prior to fixation, the culture was pre-cooled three times with phosphate buffered saline (PBS). The cells were then fixed with methanol for 15 minutes, stained with crystal violet for 20 minutes, and rinsed with water. The dishes were air dried, and the number of visible clones was visually counted. The colony formation rate was calculated. This entire procedure was repeated three times to ensure reproducibility.

Transwell assay

The cells were collected, resuspended in serum-free media, and introduced into the upper compartment of a Transwell membrane filter that had been coated with Matrigel (Corning) for invasion assays. To the lower compartment, we added a culture medium containing 10% FBS and either 0, 5, or 10 nM Tanespimycin as a chemoattractant. After a 36-hour incubation period, the cells were fixed with methanol, stained with 0.1% crystal violet, and then imaged and counted using an Olympus microscope (Tokyo, Japan). For the migration assay, the process was repeated for 24 hours.

Statistical analysis

The Wilcoxon rank-sum test was employed to conduct statistical analysis on the expression of KLRB1 in both the healthy and BRCA groups. Individuals were classified into two groups as per their “median” expression of KLRB1. The clinical and pathological characteristics of KLRB1 were assessed utilizing the Wilcoxon-rank sum test or Kruskal-Wallis test and logistic regression. Prognosis-predictive analysis was conducted utilizing Kaplan-Meier analysis as well as univariate and multivariate Cox analyses. The diagnostic value of differentially expressed genes (DEGs) was analyzed by generating a receiver operating characteristic (ROC) curve utilizing the “proc” package.


Results

Expression analysis of KLRB1 in pan-cancer and BRCA

Data downloaded from TCGA and Genotype-Tissue Expression (GTEX) were used to evaluate the expression of KLRB1 in 33 cancers. The results demonstrated that KLRB1 exhibited low expression in various cancer types, including BRCA, bladder urothelial carcinoma (BLCA), kidney chromophobe (KICH), colon adenocarcinoma (COAD), pancreatic adenocarcinoma (PAAD), liver hepatocellular carcinoma (LIHC), head and neck squamous cell carcinoma (HNSC), lung adenocarcinoma (LUAD), rectum adenocarcinoma (READ), lung squamous cell carcinoma (LUSC), thyroid carcinoma (THCA) and uterine corpus endometrial carcinoma (UCEC). However, the expression of KLRB1 was high in kidney renal clear cell carcinoma (KIRC), glioblastoma multiforme (GBM), and kidney renal papillary cell carcinoma (KIRP) (Figure 1A). The link between KLRB1 expression and clinical outcomes of individuals with BRCA was further investigated. Survival analysis demonstrated remarkable variations among distinct cancer types (Figure 1B-1D). Within the BRCA cohort, individuals exhibiting elevated KLRB1 levels displayed extended OS, progression-free interval (PFI), and disease-specific survival (DSS) in contrast to those with lowered KLRB1 levels. Furthermore, the evaluation of KLRB1 expression in BRCA within the TCGA database provided confirmation of its lower expression in this context (Figure 1E,1F). KLRB1 messenger RNA (mRNA) expression in human epidermal growth factor receptor 2 (HER2), Luminal A, Luminal B and triple negative breast cancer (TNBC) tissues were no significant difference (Figure 1G). And gene deletion was an important factor for KLRB1 down-regulation in BRCA (Figure 1H).

Figure 1 Association between KLRB1 mRNA expression level and prognosis based on TCGA database. (A) The mRNA expression of KLRB1 in distinct cancer tissues and adjoining healthy tissues. (B) Prognostic correlation between KLRB1 expression and distinct cancer types (OS). (C) Prognostic correlation between KLRB1 expression and distinct cancer types (DSS). (D) Prognostic association between KLRB1 expression and various cancer types (PFI). (E) KLRB1 mRNA expression in BRCA tissues and healthy tissues. (F) KLRB1 mRNA expression in BRCA tissues and paired sample tissues [right represents HR >1 (risky); left represents HR <1 (protective)]. (G) KLRB1 mRNA expression in HER2, luminal A, luminal B and TNBC tissues. (H) Putative copy-number alterations of KLRB1 in BRCA. *, P<0.05; **, P<0.01; ***, P<0.001. mRNA, messenger RNA; TCGA, The Cancer Genome Atlas; OS, overall survival; PFI, progression-free interval; DSS, disease-specific survival; BRCA, breast cancer; HR, hazard ratio; CI, confidence interval; TPM, transcripts per kilobase million; HER2, human epidermal growth factor receptor 2; TNBC, triple negative breast cancer.

Clinical correlation of KLRB1 expression in individuals with BRCA

The clinical features and gene expression profiles of 1083 individuals with primary BRCA were acquired from the TCGA database. Individuals were classified into high (n=542) and low (n=541) KLRB1 expression groups. The aim was to examine the link between the KLRB1 expression and the clinical and pathological attributes of individuals. The analysis demonstrated a link between KLRB1 expression and M stage (P=0.043) as well as age (P<0.001), utilizing the chi-square test or Fisher’s exact test (Table 1).

Table 1

KLRB1 expression in BRCA patients with different clinical parameters

Characteristics Low expression of KLRB1 (n=541) High expression of KLRB1 (n=542) P
T stage, n (%) 0.371
   T1 132 (12.2) 145 (13.4)
   T2 321 (29.7) 308 (28.5)
   T3 64 (5.9) 75 (6.9)
   T4 21 (1.9) 14 (1.3)
N stage, n (%) 0.288
   N0 268 (25.2) 246 (23.1)
   N1 173 (16.3) 185 (17.4)
   N2 52 (4.9) 64 (6.0)
   N3 33 (3.1) 43 (4.0)
M stage, n (%) 0.043
   M0 447 (48.5) 455 (49.3)
   M1 15 (1.6) 5 (0.5)
Pathologic stage, n (%) 0.070
   Stage I 85 (8.0) 96 (9.1)
   Stage II 321 (30.3) 298 (28.1)
   Stage III 110 (10.4) 132 (12.5)
   Stage IV 13 (1.2) 5 (0.5)
Race, n (%) 0.204
   Asian 34 (3.4) 26 (2.6)
   Black or African American 97 (9.8) 84 (8.5)
   White 361 (36.3) 392 (39.4)
Age (years), n (%) <0.001
   ≤60 267 (24.7) 334 (30.8)
   >60 274 (25.3) 208 (19.2)
PR status, n (%) 0.436
   Negative 163 (15.8) 179 (17.3)
   Indeterminate 1 (0.1) 3 (0.3)
   Positive 346 (33.5) 342 (33.1)
ER status, n (%) 0.165
   Negative 107 (10.3) 133 (12.9)
   Indeterminate 1 (0.1) 1 (0.1)
   Positive 403 (38.9) 390 (37.7)
HER2 status, n (%) 0.495
   Negative 255 (35.1) 303 (41.7)
   Indeterminate 6 (0.8) 6 (0.8)
   Positive 80 (11.0) 77 (10.6)
Age (years), median [IQR] 61 [51, 70] 55 [47, 64] <0.001

BRCA, breast cancer; PR, progesterone receptor; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; IQR, interquartile range.

Link between KLRB1 expression and survival prognosis of individuals with BRCA

Univariate and multivariate Cox analyses were conducted to examine the impact of various factors on the OS of BRCA patients, as detailed in Table 2. In the univariate Cox analysis, KLRB1 expression (P<0.001), T3&T4 stage (P=0.006), N stage (P<0.001), M1 stage (P<0.001), pathological stage III&IV (P<0.001), and age >60 (P<0.001) were linked to the OS. The multivariate Cox model revealed an association with poor prognosis for age >60 (P<0.001), estrogen receptor (ER) status positive (P=0.033), and KLRB1 expression (P=0.003) (Table 2). Furthermore, the link between KLRB1 expression and OS, DSS, and PFI in individuals with BRCA was investigated. The Kaplan-Meier (KM) diagram illustrated that elevated KLRB1 expression was associated with a poorer prognosis for OS [hazard ratio (HR) 0.55, 95% confidence interval (CI): 0.40–0.76, P<0.001] (Figure 2A). Regarding DSS, individuals with elevated KLRB1 levels still exhibited a poorer prognosis (HR 0.51, 95% CI: 0.33–0.79, P=0.003) (Figure 2B). Similarly, for PFI, individuals with elevated KLRB1 expression also experienced a poorer prognosis (HR 0.57, 95% CI: 0.41–0.79, P<0.001) (Figure 2C). However, the low expression of KLRB1 has no significant difference in the prognosis of BRCA patients with different subtypes (Figure 2D). Furthermore, ROC curve analysis was conducted to assess the capability of differentiating BRCA tissues from healthy breast tissues as per KLRB1 expression levels. The area under the ROC curve (AUC) was 0.712 (Figure 2E). Hence, KLRB1 may become a promising prognostic biological marker for patients with BRCA.

Table 2

Univariate analysis and multivariate analysis of the correlation between clinicopathological characteristics and OS in BRCA

Characteristics Total (N) Univariate analysis Multivariate analysis
Hazard ratio (95% CI) P value Hazard ratio (95% CI) P value
Pathologic T stage 1,083 0.023
   T1 277 Reference Reference
   T2 631 1.334 (0.889–2.003) 0.164 0.904 (0.372–2.199) 0.824
   T3 & T4 175 1.931 (1.208–3.088) 0.006 2.210 (0.740–6.604) 0.156
Pathologic N stage 1,067 <0.001
   N0 516 Reference Reference
   N1 358 1.947 (1.322–2.865) <0.001 1.480 (0.686–3.193) 0.317
   N2 116 2.522 (1.484–4.287) <0.001 1.265 (0.349–4.590) 0.720
   N3 77 4.191 (2.318–7.580) <0.001 2.835 (0.794–10.117) 0.108
Pathologic M stage 925 <0.001
   M0 905 Reference Reference
   M1 20 4.266 (2.474–7.354) <0.001 1.796 (0.613–5.264) 0.286
Pathologic stage 1,062 <0.001
   Stage I 181 Reference Reference
   Stage II 619 1.703 (0.989–2.933) 0.055 0.948 (0.289–3.118) 0.931
   Stages III & IV 262 3.566 (2.042–6.228) <0.001 1.980 (0.338–11.606) 0.449
Age (years) 1,086 <0.001
   ≤60 603 Reference Reference
   >60 483 2.024 (1.468–2.790) <0.001 3.326 (1.972–5.612) <0.001
PR status 1,033 0.068
   Negative 342 Reference Reference
   Positive 691 0.729 (0.521–1.019) 0.065 0.972 (0.434–2.176) 0.945
ER status 1,036 0.070
   Negative 240 Reference Reference
   Positive 796 0.709 (0.493–1.019) 0.063 0.394 (0.167–0.927) 0.033
HER2 status 717 0.074
   Negative 560 Reference Reference
   Positive 157 1.593 (0.973–2.609) 0.064 1.019 (0.564–1.840) 0.950
KLRB1 1,086 <0.001
   Low 543 Reference Reference
   High 543 0.550 (0.396–0.763) <0.001 0.476 (0.290–0.780) 0.003

OS, overall survival; BRCA, breast cancer; CI, confidence interval; PR, progesterone receptor; ER, estrogen receptor; HER2, human epidermalgrowth factor receptor 2.

Figure 2 The survival rate of individuals with BRCA with elevated and reduced expression levels of KLRB1. (A) OS. (B) DSS. (C) PFI. (D) No significant difference in the prognosis of different breast cancer subtypes in breast cancer patients with low KLRB1 expression. (E) ROC analysis showed that KLRB1 could accurately distinguish BRCA tumor tissues from healthy tissues. HR, hazard ratio; OS, overall survival; PFI, progression-free interval; DSS, disease-specific survival; BRCA, breast cancer; ROC, receiver operating characteristic.

Survival analysis

Subsequently, univariate and multivariate analyses were conducted. In the former, reduced expression of T3 and T4 within the T stage, N1, N2, and N3 within the N stage, M1 within the M stage, stages 3 and 4 within the pathological stage, age >60, and KLRB1 were linked to OS. The subsequent multivariate analysis indicated independent risk factors. Specifically, age >60, ER status Positive, and reduced expression of KLRB1 were identified as independent predictive factors for OS among inpatients with BRCA (Table 2 and Figure 3).

Figure 3 Univariate and multivariate survival analysis. (A) Univariate analysis of OS of individuals with BRCA. (B) Multivariate analysis of OS of individuals with BRCA (P value: log-rank test). HR, hazard ratio; CI, confidence interval; PR, progesterone receptor; ER, estrogen receptor; OS, overall survival; BRCA, breast cancer.

Enrichment analysis of KLRB1-related genes

A total of 24,593 genes exhibited differential expression between the groups characterized by low and high KLRB1 expression levels, including 8 genes with lowered expression levels and 20 genes with elevated expression levels (adjusted P value <0.05, |log2 fold change (FC)|>3) (Figure 4A and table available at https://cdn.amegroups.cn/static/public/tcr-23-1231-1.xlsx). The results of GO and KEGG joint analysis of DEGs demonstrated that it was mainly enriched in signaling receptor activator activity, lymphocyte proliferation, mononuclear cell proliferation, leucocyte proliferation, receptor-ligand activity, immunoglobulin binding and hematopoietic cell lineage signaling pathways (Figure 4B and Table 3). Moreover, the GSEA of the detected DEGs revealed several immune-related biological processes. These included KEGG OLFACTORY TRANSDUCTION, REACTOME OLFACTORY SIGNALING PATHWAY, NABA SECRETED FACTORS, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION and KEGG SYSTEMIC LUPUS ERYTHEMATOSUS (Figure 4C). Next, the correlation between the top 10 upregulated and downregulated DEGs and KLRB1 was examined, revealing significant associations between the majority of DEGs and KLRB1 (Figure 4D-4E).

Figure 4 Functional enrichment analysis of KLRB1-related DEGs and KLRB1 in BRCA. (A) Volcano plot. Blue dots and red dots denote DEGs with remarkably reduced and enhanced expression, respectively. (B) GO and KEGG joint analysis. (C) GSEA analysis. (D) Heatmap of the relationship between KLRB1 expression and the top 10 upregulated DEGs. (E) Heatmap of the association between KLRB1 expression and the top 10 downregulated DEGs. *, P<0.05; **, P<0.01; ***, P<0.001. DEGs, differentially expressed genes; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; GSEA, gene set enrichment analysis.

Table 3

The results of GO and KEGG joint analysis of DEGs

Ontology ID Description Gene ratio Bg ratio P value P.adjust Z score
BP GO:0046651 Lymphocyte proliferation 7/23 296/18,800 4.41e−08 1.91e−05 2.6457513
BP GO:0032943 Mononuclear cell proliferation 7/23 300/18,800 4.84e−08 1.91e−05 2.6457513
BP GO:0070661 Leukocyte proliferation 7/23 330/18,800 9.28e−08 2.36e−05 2.6457513
CC GO:0098992 Neuronal dense core vesicle 2/23 13/19,594 0.0001 0.0049 −1.4142136
CC GO:0031045 Dense core granule 2/23 26/19,594 0.0004 0.0101 −1.4142136
CC GO:0043204 Perikaryon 3/23 153/19,594 0.0007 0.0118 −0.5773503
MF GO:0048018 Receptor ligand activity 5/20 489/18,410 0.0001 0.0051 −0.4472136
MF GO:0030546 Signaling receptor activator activity 5/20 496/18,410 0.0002 0.0051 −0.4472136
MF GO:0019865 Immunoglobulin binding 2/20 24/18,410 0.0003 0.0067 1.4142136
KEGG hsa04640 Hematopoietic cell lineage 3/12 99/8,164 0.0004 0.0116 1.7320508

GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEG, differentially expressed gene; BP, biological process; CC, cellular component; MF, molecular function.

Link between KLRB1 expression and immune cell infiltration

Additionally, an assessment was conducted to determine if a link existed between KLRB1 expression levels and the infiltration status of immune cells. We used ssGSEA from the R package and R from Spearman to study the potential association between KLRB1 expression levels and 24 immune cell types. The findings indicated a substantial link between KLRB1 expression and all immune cells (Figure 5A). Furthermore, heatmap visualization aided in evaluating and illustrating the varying degrees of correlation among the ratios of 24 distinct tumor-infiltrating immune cell subsets (Figure 5B).

Figure 5 KLRB1 expression was associated with immune cell infiltration. (A) Lollipop chart of KLRB1 expression levels in 24 immune cell types. (B) Heatmap of 24 infiltrating immune cells in BRCA and KLRB1 have the pivotal function in the immune infiltration in BRCA. *, P<0.05; **, P<0.01; ***, P<0.001. BRCA, breast cancer.

Nomogram development and validation utilizing the independent factors

A nomogram was developed utilizing independent OS-related factors to enable the prognosis prediction of individuals with BRCA. This predictive tool assigns a higher total score to patients with a less favorable prognosis (Figure 6A). To evaluate the prognosis-predictive capacity of the nomogram, calibration curves were employed (Figure 6B), confirming its effectiveness in prognosis prediction.

Figure 6 A nomogram and calibration curves for the prediction of one-, three-, and five-year OS rates of individuals with BRCA. (A) A nomogram for the prediction of the one-, three-, and five-year OS rates of individuals with BRCA. (B) Calibration curves of the nomogram prediction of one-, three-, and five-year OS rates of individuals with BRCA. OS, overall survival; BRCA, breast cancer.

High expression of KLRB1 in BRCA

For assessing the potential utility of KLRB1 as a biological marker for BRCA, the expression of KLRB1 in BRCA tissues was further verified using qPCR and IHC. Both qPCR and immunohistochemical outcomes indicated diminished KLRB1 expression in BRCA (Figure 7A,7B). Subsequently, the MCF7 cell line was transfected with a KLRB1-targeted pEZ-M03 vector. CCK8 assay showed that the proliferation of MCF7 cells decreased after transfection with KLRB1 (Figure 7C). Next, we evaluated the expression of KLRB1 in MCF10A cell line, MCF7 cell line and MDAMB231 cell line, and found that the expression of KLRB1 in MCF7 cell line and MDAMB231 cell line was significantly lower than that in MCF10A cell line (Figure 8A). qPCR detection of MCF7 cell lines and MDAMB231 cell lines transfected with KLRB1 targeted pez-m03 vector showed that the expression of KLRB1 in the cell lines transfected with KLRB1 was significantly higher than that in the cell lines transfected with vector (Figure 8B,8C). CCK8 assay and colony formation assay showed that the proliferation of MDAMB231 cell line decreased after transfection of KLRB1 (Figure 8D,8E). Transwell assay showed that the migration and invasion ability of MDAMB231 cell line decreased after transfected with KLRB1 (Figure 8F).

Figure 7 BRCA exhibits lowered expression levels of KLRB1. (A) The expression of KLRB1 mRNA was assessed by qPCR. (B) The expression of KLRB1 proteins was assessed by IHC. (Magnification: ×40). (C) Decreased proliferation of MCF7 cells transfected with KLRB1 vector. *P<0.05. BRCA, breast cancer; mRNA, messenger RNA; qPCR, quantitative polymerase chain reaction; IHC, immunohistochemistry.
Figure 8 Overexpression of KLRB1 inhibits the progression of breast cancer cells. (A) The expression of KLRB1 in MCF10A cells, MCF7 cells and MDAMB231 cells. (B,C) The expression level of KLRB1 after transfection in MCF7 cells and MCF10A cells. (D,E) Decreased proliferation of MDAMB231 cells transfected with KLRB1 vector (0.1% crystal violet staining). (F) KLRB1 inhibits the migration and invasion ability of both MCF7 and MDAMB231 cells (0.1% crystal violet staining, ×10). *, P<0.05.

Discussion

BRCA poses a significant threat to the health of women, being the most prevalent cancer and the second major contributor to cancer-related mortality among females (15,16,17). Therefore, there is a pressing need to identify precise biological markers that can facilitate early detection and continuous monitoring of disease progression. As previous research has indicated, the EMC (ER membrane protein complex subunit) is critically involved in the onset and progression of human cancer (18,19). Limited research has explored the link between the expression of KLRB1 and the prognosis of BRCA. This study delved into the potential mechanism governing the role of KLRB1 in promoting BRCA, as well as its feasibility as a potential molecular biological marker.

The comprehensive pan-cancer analysis revealed the consistent downregulation of KLRB1 across various cancer types. Notably, elevated KLRB1 expression correlated with improved OS in individuals with BRCA. Analysis of various clinical stages revealed a substantial correlation between KLRB1 expression and clinical stages. Univariate and multivariate Cox analyses affirmed the independent prognosis-predictive value of KLRB1 in predicting the prognosis of individuals. Collectively, these findings, along with the ROC analysis outcomes, strongly imply that KLRB1 holds promise as a potential prognostic biological marker for individuals with BRCA.

This study revealed a significant inhibitory effect of the KLRB1 gene on cell proliferation in BRCA cells. Simultaneously, this research aims to ascertain the association between the expression of the KLRB1 gene and the clinical prognosis of individuals with BRCA, indicating that individuals with higher KLRB1 expression experience a more favorable prognosis. These findings will serve as a crucial foundation for further investigating the mechanism of the KLRB1 gene in BRCA and identifying potential therapeutic targets.

The results of GSEA suggested that KLRB1-related differential genes were involved in KEGG organic transformation, Reactome organic signaling pathway, NABA restricted factors, KEGG cytokine-cytokine receptor interaction, and KEGG systemic lupus erythematosus pathways. These pathways widely impact cell proliferation, migration, differentiation, and metabolism. In BRCA, olfactory transduction mediated signal transduction ultimately leads to olfactory perception by recognizing odor molecules and activating signal transduction pathways, which also regulates the apoptotic cycle of olfactory sensory neurons in an olfactory receptor-specific manner. A recent study has indicated that certain olfactory receptors exhibit expression in tissues other than the olfactory epithelium, implying their potential for pleiotropic effects (20). In addition, the cytokine-cytokine receptor interaction signaling pathway is also related to BRCA treatment. Various methods can enhance the growth inhibitory and immunostimulatory effects of interferon and interleukin or inhibit the inflammatory and tumor effects of cytokines, thereby treating BRCA (21,22).

Furthermore, the link between KLRB1 expression and the level of immune infiltration in BRCA was investigated utilizing two approaches, ssGSEA and Spearman. KLRB1 exhibited the highest positive correlation with T cells and cytotoxic cells. T cells are a major subclass of lymphocytes, possessing diverse biological functions, including directly targeting and killing specific cells, aiding or inhibiting antibody production by B cells, responding to specific antigens and mitogens, and generating cytokines (23). Research has demonstrated that T cells can directly inhibit BRCA cells and improve the prognosis of BRCA individuals (24,25). Cytotoxic T lymphocyte (CTL) is a specific T cell that secretes various cytokines to participate in immunity and has a strong anti-tumor effect (26). Study has shown that CTL can effectively inhibit BRCA cells and inhibit the onset and angiogenesis of BRCA (27).

Finally, the results were validated by qPCR, IHC, and CCK8 assays. The study demonstrated a significant decrease in KLRB1 expression in corresponding non-tumor tissues. Additionally, the enhanced expression of KLRB1 led to a decrease in the proliferation and invasion capacity of BRCA MCF7 cells. These collective findings highlight that KLRB1 holds promise as a potential predictive tumor marker for individuals with BRCA.

In conclusion, the study aimed to investigate the mechanism and potential therapeutic targets associated with the KLRB1 gene in BRCA. Through the examination of KLRB1 gene expression and function, the aim is to unveil its crucial involvement in the onset and development of BRCA. This endeavor also aspires to offer novel approaches and techniques for addressing the treatment of BRCA. Nonetheless, the precise mechanism via which KLRB1 influences the tumor immune microenvironment and the progression of tumors in BRCA remains to be fully understood. Additional fundamental research and clinical trials are warranted to comprehensively unravel the biological impacts of KLRB1 in BRCA.


Conclusions

In summary, the elevated expression level of KLRB1 is related to prognostic significance and KLRB1 is positively linked to T cells and cytotoxic cells. Consequently, KLRB1, potentially linked to immune infiltration, could serve as a predictive indicator for individuals with BRCA.


Acknowledgments

Funding: This work was supported by the Natural Science Foundation of Liaoning Province (No. 2019-ZD-1020).


Footnote

Reporting Checklist: The authors have completed the TRIPOD reporting checklist. Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1231/rc

Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1231/dss

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Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1231/coif). The authors report funding from the Natural Science Foundation of Liaoning province (No. 2019-ZD-1020). The authors have no other conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. The study was conducted in accordance with the Declaration of Helsinki (as revised in 2013).The approval for this research was granted by the ethics committee of Liaoning Cancer Hospital (20210621) and written informed consent was obtained from every participant.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.


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Cite this article as: Liu X, Cui Q, Qin N. Low expression of KLRB1 predicts poor survival outcomes and is associated with immune infiltration in breast cancer. Transl Cancer Res 2024;13(3):1225-1240. doi: 10.21037/tcr-23-1231

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