Genomic Analysis Uncovers Immune Microenvironment Characteristics and Drug Sensitivity of Ferroptosis in Breast Cancer Brain Metastasis

Identification of CISD1 as a Prognostic Biomarker for Breast Cancer

Background

Although CISD1 (CDGSH iron sulfur domain 1) is upregulated in many cancer types, the potential role of CISD1 in breast cancer is still unclear. The purpose of this study was to investigate its clinical significance in breast cancer.

Methods

We obtained 1109 breast cancer samples and 113 normal samples from The Cancer Genome Atlas (TCGA) and GTEx databases to demonstrate the relationship between CISD1 expression and pancancer characteristics. We analysed the relationship between CISD1 and breast cancer using the t-test and the chi-square test to evaluate the expression level of CISD1 and its clinical significance in breast cancer. The prognostic value of CISD1 in breast cancer was determined by Kaplan‒Meier and Cox regression analyses. The biological pathways were screened by gene set analysis and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and single-sample gene set enrichment analysis (ssGSEA), of which the correlation between the level of immune infiltration and the expression of CISD1 in breast cancer was then analysed. Finally, we verified the conclusion by qPCR, immunohistochemistry, and CCK8.

Results

CISD1 is highly expressed in breast cancer patients. In addition, we verified a higher expression of CISD1 expressed in the BRCA (breast cancer) cell line, whereas CISD1 has a high diagnostic value, with an AUC of 0.718. Kaplan‒Meier survival and Cox regression analyses showed that high expression of CISD1 was independently associated with adverse clinical outcomes. In turn, GO and KEGG analyses showed that most genes were related to rRNA metabolic process, rRNA processing. Moreover, PCR and immunohistochemistry showed that CISD1 in breast cancer tissues was upregulated significantly, with CCK8 results showing that the proliferation of breast cancer cells decreased after CISD1 knockout.

Conclusion

A high level of CISD1 is associated with poor prognosis and immune infiltration in breast cancer.

Targeting ferroptosis, the achilles' heel of breast cancer: A review

Ferroptosis is referred as a novel type of cell death discovered in recent years with the feature of the accumulation of iron-dependent lipid reactive oxygen species. Breast cancer is one of the most common malignant cancers in women. There is increasing evidence that ferroptosis can inhibit breast cancer cell growth, improve the sensitivity of chemotherapy and radiotherapy and inhibit distant metastases. Therefore, ferroptosis can be regarded a new target for tumor suppression and may expand the landscape of clinical treatment of breast cancer. This review highlights the ferroptosis mechanism and its potential role in breast cancer treatment to explore new therapeutic strategies of breast cancer.

Low expression of PEBP1P2 promotes metastasis of clear cell renal cell carcinoma by post-transcriptional regulation of PEBP1 and KLF13 mRNA

Background

Pseudogenes play an essential role in tumor occurrence and progression. However, the functions and mechanisms of pseudogenes in clear cell renal cell carcinoma (ccRCC) remain largely elusive.

Methods

We quantified PEBP1P2 expression in ccRCC tissues and cells using fluorescence in situ hybridization and real-time PCR. Besides, we evaluated the role of PEBP1P2 in ccRCC using a lung metastasis model and a transwell assay. Finally, we documented the interactions between PEBP1P2, PEBP1, and KLF13 by performing luciferase, RNA immunoprecipitation, RNA pulldown, and targeted RNA demethylation assays.

Results

Low PEBP1P2 expression correlates significantly with advanced stages and poor prognosis in ccRCC patients. Besides, PEBP1P2 overexpression inhibits ccRCC metastasis formation in vivo and in vitro. Interestingly, PEBP1P2 directly interacted with 5-methylcytosine (m5C)-containing PEBP1 mRNA and recruited the YBX1/ELAVL1 complex, stabilizing PEBP1 mRNA. In addition, PEBP1P2 increased KLF13 mRNA levels by acting as a sponge for miR-296, miR-616, and miR-3194.

Conclusions

PEBP1P2 inhibits ccRCC metastasis formation and regulates both PEBP1 and KLF13. Therefore, molecular therapies targeting PEBP1P2 might be an effective treatment strategy against ccRCC and other cancers with low PEBP1P2 levels.

LPCAT3 is a potential prognostic biomarker and may be correlated with immune infiltration and ferroptosis in acute myeloid leukemia: a pan-cancer analysis

BACKGROUND

Recent studies have highlighted the critical role of lysophosphatidylcholine acyltransferase 3 (LPCAT3) during cancer development. However, the abnormal expression and prognostic significance of pan-cancer have not been determined.

METHODS

We explored the expression level and prognostic value of LPCAT3 in 33 cancers by bioinformatics techniques, and comprehensively studied the biological function and immune infiltration based on the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases as well as many online websites.

RESULTS

LPCAT3 is significantly upregulated in many cancers, and it is associated with prognosis. Pan-cancer Cox regression analysis indicated that the high expression of LPCAT3 was associated with poor prognosis in acute myeloid leukemia (AML), lower-grade glioma (LGG), ovarian cancer (OV), and uveal melanoma (UVM), while better prognosis in kidney renal clear cell carcinoma (KIRC) (all P<0.05). Further analysis indicated that higher LPCAT3 expression in most cancers markedly decreased the infiltration of immune cells, except diffuse large B-cell lymphoma (DLBC), AML, LGG, stomach adenocarcinoma (STAD), and UVM. In contrast, the expression level of LPCAT3 was positively correlated with most immune checkpoints in colon adenocarcinoma (COAD), DLBC, LGG, liver hepatocellular carcinoma (LIHC), and UVM. Additionally, LPCAT3 expression was associated with tumor mutational burden (TMB) in 4 cancer types, while microsatellite instability (MSI) was in 3 cancer types. Functional enrichment analysis showed LPCAT3 upregulation was highly associated with lipid metabolism and ferroptosis processes. In addition, the result of prediction drug response suggested that B-cell lymphoma 2 (BCL2) inhibitors and Midostaurin may be a potential treatment option for AML with low-LPCAT3 expression.

CONCLUSIONS

LPCAT3 expression is increased in multiple cancers. Overexpression of LPCAT3 is associated with poor prognosis and tumor immune microenvironment in many cancers, especially in AML. Our results showed that the oncogene of LPCAT3 may serve as a potential prognostic biomarker and/or therapeutic target in AML patients.

The cuproptosis-related signature predicts prognosis and indicates immune microenvironment in breast cancer

Breast cancer (BC) is the most diagnosed cancer in women. Cuproptosis is new regulated cell death, distinct from known death mechanisms and dependent on copper and mitochondrial respiration. However, the comprehensive relationship between cuproptosis and BC is still blank until now. In the present study, we acquired 13 cuproptosis-related regulators (CRRs) from the previous research and downloaded the RNA sequencing data of TCGA-BRCA from the UCSC XENA database. The 13 CRRs were all differently expressed between BC and normal samples. Using consensus clustering based on the five prognostic CRRs, BC patients were classified into two cuproptosis-clusters (C1 and C2). C2 had a significant survival advantage and higher immune infiltration levels than C1. According to the Cox and LASSO regression analyses, a novel cuproptosis-related prognostic signature was developed to predict the prognosis of BC effectively. The high- and low-risk groups were divided based on the risk scores. Kaplan-Meier survival analysis indicated that the high-risk group had shorter overall survival (OS) than the low-risk group in the training, test and entire cohorts. GSEA indicated that the immune-related pathways were significantly enriched in the low-risk group. According to the CIBERSORT and ESTIMATE analyses, patients in the high-risk group had higher infiltrating levels of antitumor lymphocyte cell subpopulations and higher immune score than the low-risk group. The typical immune checkpoints were all elevated in the high-risk group. Furthermore, the high-risk group showed a better immunotherapy response than the low-risk group based on the Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenoscore (IPS). In conclusion, we identified two cuproptosis-clusters with different prognoses using consensus clustering in BC. We also developed a cuproptosis-related prognostic signature and nomogram, which could indicate the outcome, the tumor immune microenvironment, as well as the response to immunotherapy.