High BRCA1 expression is an independent prognostic biomarker in LUAD and correlates with immune infiltration

Lung adenocarcinoma (LUAD) patients with elevated breast cancer susceptibility gene 1 (BRCA1) expression had markedly worse overall survival and progression‐free survival compared to those with reduced BRCA1 levels. In contrast, BRCA1 expression did not correlate with survival outcomes in squamous cell carcinoma patients. The overexpression of BRCA1 was an independent risk factor for LUAD and was indicative of an immune‐suppressive tumor microenvironment.


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Non-small-cell lung cancer (NSCLC) is the primary histopathological subtype of lung cancer and accounts for around 82% of all pulmonary neoplasms [1].Breast cancer susceptibility gene 1 (BRCA1) is a tumor suppressor gene that regulates cellular responses to stress through DNA damage repair and is frequently mutated in breast and ovarian cancers [2].Furthermore, previous studies have increasingly shown that the expression of BRCA1 and the relevant poly (ADPribose) polymerase inhibitors is related to the prognosis and therapeutic response of other tumors, including lung cancer [3,4].However, previous findings on the prognostic value of BRCA1 for NSCLC have been inconsistent or conflicting, which may be attributed to the small number of patients from a single center or disparity in the ratio of patients with lung adenocarcinoma (LUAD) versus squamous cell carcinoma (LUSC) [5].The aim of this study was to determine the prognostic value of BRCA1 in NSCLC and its association with immune infiltration.
In this study, the clinicopathological, survival, immune infiltration, and BRCA1 expression data of lung cancer patients retrieved from public databases and relevant articles were analyzed.The results demonstrated that BRCA1 RNA and protein levels were significantly upregulated in LUSC and LUAD tissue compared to normal lung tissue (Figure 1a,b).Although BRCA1 expression showed no significant correlation with the overall survival (OS) or Abbreviations: BRCA1, breast cancer susceptibility gene 1; DEGs, differentially expressed genes; GO, Gene Ontology; iDCs, induced dendritic cells; LUAD, lung adenocarcinoma; LUSC, squamous cell carcinoma; NSCLC, non-small-cell lung cancer; OS, overall survival; PFS, progression-free survival; ROC, receiver operating characteristic.

F I G U R E 1 (See caption on next page)
progression-free survival (PFS) in the overall lung cancer cohort, LUAD patients with elevated BRCA1 expression had a markedly worse OS and PFS compared to those with reduced BRCA1 levels.In contrast, BRCA1 expression did not correlate with survival outcomes in LUSC patients (Figure 1c,d).The analysis of the Gene Expression Omnibus data set (GSE41271) revealed a similar association between high BRCA1 expression and a shorter OS and PFS in LUAD (Figure 1e,f).
To further verify the abovementioned results, a systematic meta-analysis was performed.As shown in Supporting Information: Figure S1 and Table S1, a total of 1340 potential articles were initially retrieved from PubMed, Embase, the Cochrane Library, and Web of Science data sets.The general characteristics of the 17 eligible publications involving 19 studies are shown in Supporting Information: Table S2.Data of 2765 patients, comprising 1962 males and 802 females (the gender of one patient was not given), were included in the pooled analysis.All cases were diagnosed with NSCLC, and 12 studies focused on LUAD patients, whereas 7 studies primarily included LUSC patients.The results of the meta-analysis indicated that increased BRCA1 portended a poor OS and PFS in patients with LUAD (Figure 1g,h).In contrast, no correlation was observed between BRCA1 expression and prognosis in LUSC (Figure 1g,h).Due to the significant heterogeneity across the included studies, the combined hazard ratio of OS and PFS was calculated based on a random-effects model (Figure 1g,h).Results of sensitivity analysis, meta-regression, and publication bias are presented in supplementary materials (Supporting Information: Figures S2,3 and Tables S3,4).
Subsequently, the baseline clinicopathological information of The Cancer Genome Atlas (TCGA)-LUAD was integrated and analyzed and exploratory analysis was conducted to fully explore its further application in clinical practice (Supporting Information: Table S5).The Cox multivariate model constructed using BRCA1 expression and other related prognostic factors demonstrated that high BRCA1 expression was an independent predictor for adverse OS in LUAD (Figure 1i, Supporting Information: Table S5).Moreover, the receiver operating characteristic (ROC) curve analysis suggested a robust diagnostic value of BRCA1 in discriminating LUAD from healthy samples (Figure 1j).Univariate logistic regression further revealed that BRCA1 overexpression was more likely in LUAD patients ≤65 years of age and with advanced tumor stage, lymph node involvement, metastasis, or advanced stage (Figure 1k).Moreover, in verifying the prognostic observation of BRCA1, the association between BRCA1 expression and OS in LUAD patients was analyzed by tissue microarray.Immunohistochemical staining indicated that high expression of BRCA1 portended a shorter OS and was an independent prognostic factor in LUAD (Supporting Information: Table S7, Figure 1l,n).
To further explore the mechanisms underlying the prognostic role of BRCA1 in LUAD, a total of 7240 differentially expressed genes (DEGs) were screened between the BRCA1 high and BRCA1 low samples, of which 6555 genes were upregulated, and 685 genes were downregulated (adjusted p < 0.05, |Log2-FC | > 1, Figure 2a).Gene Ontology (GO) enrichment analysis indicated that the DEGs were enriched in biological processes or cellular components related to gene expression and protein synthesis, such as mRNA trans splicing, formation of quadruple SL/U4/U5/U6 snRNP, and spliceosomal snRNP assembly (Figure 2b).Gene set (m) OS of high and low BRCA1 expression in patients with LUAD as shown by Kaplan-Meier survival analysis and analyzed by a log-rank test using the cohort data described in (l).(n) Cox univariate and multivariate regression analyses using the cohort data described in (l).*p < 0.05, **p < 0.01, ***p < 0.001.BRCA1, breast cancer susceptibility gene 1; CI, confidence interval; GEO, Gene Expression Omnibus; GTEx, Genotype-Tissue Expression; HPA, Human Protein Atlas; HR, hazard ratio; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; OS, overall survival; PFS, progression-free survival; ROC, receiver operating characteristic curve; TCGA, The Cancer Genome Atlas.enrichment analysis further revealed that more cell proliferation-related biological processes were enriched in the BRCA1 high group, thereby suggesting that increased BRCA1 expression conferred a growth advantage to LUAD cells (Figure 2c).Furthermore, the expression of BRCA1 negatively correlated with the infiltration of mast cells, CD8 + T cells, and induced dendritic cells (iDCs), whereas an inverse correlation was observed between BRCA1 and Th2 cells (Figure 2d).The enrichment scores of mast cells, CD8 + T cells, and iDCs were significantly increased in LUAD tissues with low expression compared to those with high BRCA1 expression, and the latter had a higher enrichment score of Th2 cells (Figure 2e).
Taken together, the overexpression of BRCA1 is an independent risk factor for LUAD rather than LUSC, and is indicative of an immune-suppressive tumor microenvironment.Further studies are warranted to investigate the potential role of BRCA1 as a predictor of immunotherapy response in LUAD.

1
High BRCA1 expression is an independent prognostic biomarker in lung adenocarcinoma.(a) Expression of BRCA1 mRNA in different tumor tissue types and the corresponding normal tissues from TCGA and GTEx data sets.(b) Expression of BRCA1 protein in healthy lungs (left panel), LUSC (middle panel), and LUAD (right panel) samples from the HPA project (scale bar, 50 μm).(c, d) The OS (c) and PFS (d) of BRCA1 high and BRCA1 low lung cancer (left panel), LUSC (middle panel), and LUAD (right panel) patients from the TCGA database.(e, f) The OS (e) and PFS (f) of BRCA1 high and BRCA1 low lung cancer (left panel), LUSC (middle panel), and LUAD (right panel) patients from GEO (GSE41271).(g, h) Forest plots showing the correlation between increased BRCA1 expression and clinical prognosis in the total cohort and pathological subgroups.Results are presented as average HRs with 95% CIs of OS (g) and PFS (h) for all eligible studies.(i) Forest map showing factors influencing OS outcomes of LUAD patients as per Cox regression multivariable analysis.(j) ROC curve for the discriminatory ability of BRCA1 using data of normal lung samples and LUAD samples from TCGA database.(k) Logistic regression analysis of the correlation between BRCA1 expression and clinicopathological features of patients with LUAD.(l) Representative images of immunohistochemical staining for BRCA1 in LUAD tissues with high (top panel) and low (lower panel) expression of BRCA1 (scale bar, 200 μm).

F I G U R E 2
Increase in BRCA1 expression correlates with immune infiltration in lung adenocarcinoma.(a) Volcano plot showing DEGs between BRCA1 high and BRCA1 low groups.(b) GO term enrichment analysis of DEGs.(c) Results of GSEA on the Hallmark gene sets archived in MSigDB.(d) Association of BRCA1 expression with the relative abundance of different immune cell populations.The size of the diamond represents Spearman's correlation coefficient value.(e) Infiltration levels of the four most significantly different immune cells between BRCA1 high and BRCA1 low groups.From left to right: mast cells, CD8 + T cells, iDCs, and Th2 cells.***p < 0.001.BRCA1, breast cancer susceptibility gene 1; DC, induced dendritic cell; DEG, differentially expressed gene; GESA, gene set enrichment analysis; GO, Gene Ontology; LUAD, lung adenocarcinoma; MSigDB, Molecular Signatures database.[Correction added on 20 April 2023, after first publication: The figure 2 was revised for clarity at the request of the author.]