Low expression of SLC22A18 predicts poor survival outcome in patients with breast cancer after surgery

Potential of blood-based biomarker approaches in endometrium and breast cancer: a case-control comparison study

Purpose

Endometrial carcinoma is the second most common gynecological malignancy. Until today lacking a screening tool. A blood-based biomarker could help address this need.

Methods

The expression levels of 30 acylcarnitines, 18 amino acids, 6 miRNAs, and 7 DNA methylation sites were measured in blood samples from 331 women (20 EC, 14 benign uterine lesions (benign), 140 breast cancers (BC), 157 controls). Areas under the ROC curves (AUC), sensitivity (sens.) and specificity (spec.) were computed to identify the variables best distinguishing.

Results

The best top ten markers for the four comparisons (cancer vs. cancer-free; EC vs. BC, EC vs. controls; EC vs. benign), were identified via AUC. Malonylcarnitine distinguished best patients with EC from controls (AUC: 0.827, sens. 80%, spec. 73.1%) or BC (AUC: 0.819, sens. 84.3%, spec. 80%) being most notable. Tryptophan best differentiated benign from EC (AUC: 0.846, sens. 70%, spec. 92.9%).

Conclusions

The levels of the analyzed blood markers yielded promising results in the detection of EC and warrant further evaluation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00404-022-06482-8.

DCAF13 promotes breast cancer cell proliferation by ubiquitin inhibiting PERP expression

Evolutionarily conserved DDB1-and CUL4-associated factor 13 (DCAF13) is a recently discovered substrate receptor for the cullin RING-finger ubiquitin ligase 4 (CRL4) E3 ubiquitin ligase that regulates cell cycle progression. DCAF13 is overexpressed in many cancers, although its role in breast cancer is currently elusive. In this study we demonstrate that DCAF13 is overexpressed in human breast cancer and that its overexpression closely correlates with poor prognosis, suggesting that DCAF13 may serve as a diagnostic marker and therapeutic target. We knocked down DCAF13 in breast cancer cell lines using CRISPR/Cas9 and found that DCAF13 deletion markedly reduced breast cancer cell proliferation, clone formation, and migration both in vitro and in vivo. In addition, DCAF13 deletion promoted breast cancer cell apoptosis and senescence, and induced cell cycle arrest in the G1/S phase. Genome-wide RNAseq analysis and western blotting revealed that loss of DCAF13 resulted in both mRNA and protein accumulation of p53 apoptosis effector related to PMP22 (PERP). Knockdown of PERP partially reversed the hampered cell proliferation induced by DCAF13 knockdown. Co-immunoprecipitation assays revealed that DCAF13 and DNA damage-binding protein 1 (DDB1) directly interact with PERP. Overexpression of DDB1 significantly increased PERP polyubiquitination, suggesting that CRL4^DCAF13 E3 ligase targets PERP for ubiquitination and proteasomal degradation. In conclusion, DCAF13 and the downstream effector PERP occupy key roles in breast cancer proliferation and potentially serve as prognostics and therapeutic targets.

The Roles of Imprinted SLC22A18 and SLC22A18AS Gene Overexpression Caused by Promoter CpG Island Hypomethylation as Diagnostic and Prognostic Biomarkers for Non-Small Cell Lung Cancer Patients

Genomic imprinting is a process that involves one gene copy turned-off in a parent-of-origin-dependent manner. The regulation of imprinted genes is broadly dependent on promoter methylation marks, which are frequently associated with both oncogenes and tumor suppressors. The purpose of this study was to assess the DNA methylation patterns of the imprinted solute-carrier family 22 member 18 (SLC22A18) and SLC22A18 antisense (SLC22A18AS) genes in non-small cell lung cancer (NSCLC) patients to study their relevance to the disease. We found that both genes were hypomethylated in adenocarcinoma and squamous cell carcinoma patients. Due to this imprinting loss, SLC22A18 and SLC22A18AS were found to be overexpressed in NSCLC tissues, which is significantly more evident in lung adenocarcinoma patients. These results were validated through analyses of public databases of NSCLC patients. The reversed gene profile of both genes was achieved in vitro by treatment with ademetionine. We then showed that high SLC22A18 and SLC22A18AS expression levels were significantly associated with worsening disease progression. In addition, low levels of SLC22A18AS were also correlated with better overall survival for lung adenocarcinoma patients. We found that SLC22A18 and SLC22A18AS knockdown inhibits cell proliferation in vitro. All these results suggest that both genes may be useful as diagnostic and prognostic biomarkers in NSCLC, revealing novel therapeutic opportunities.

Systems biology comprehensive analysis on breast cancer for identification of key gene modules and genes associated with TNM-based clinical stages

Breast cancer (BC), as one of the leading causes of death among women, comprises several subtypes with controversial and poor prognosis. Considering the TNM (tumor, lymph node, metastasis) based classification for staging of breast cancer, it is essential to diagnose the disease at early stages. The present study aims to take advantage of the systems biology approach on genome wide gene expression profiling datasets to identify the potential biomarkers involved at stage I, stage II, stage III, and stage IV as well as in the integrated group. Three HER2-negative breast cancer microarray datasets were retrieved from the GEO database, including normal, stage I, stage II, stage III, and stage IV samples. Additionally, one dataset was also extracted to test the developed predictive models trained on the three datasets. The analysis of gene expression profiles to identify differentially expressed genes (DEGs) was performed after preprocessing and normalization of data. Then, statistically significant prioritized DEGs were used to construct protein-protein interaction networks for the stages for module analysis and biomarker identification. Furthermore, the prioritized DEGs were used to determine the involved GO enrichment and KEGG signaling pathways at various stages of the breast cancer. The recurrence survival rate analysis of the identified gene biomarkers was conducted based on Kaplan-Meier methodology. Furthermore, the identified genes were validated not only by using several classification models but also through screening the experimental literature reports on the target genes. Fourteen (21 genes), nine (17 genes), eight (10 genes), four (7 genes), and six (8 genes) gene modules (total of 53 unique genes out of 63 genes with involving those with the same connectivity degree) were identified for stage I, stage II, stage III, stage IV, and the integrated group. Moreover, SMC4, FN1, FOS, JUN, and KIF11 and RACGAP1 genes with the highest connectivity degrees were in module 1 for abovementioned stages, respectively. The biological processes, cellular components, and molecular functions were demonstrated for outcomes of GO analysis and KEGG pathway assessment. Additionally, the Kaplan-Meier analysis revealed that 33 genes were found to be significant while considering the recurrence-free survival rate as an alternative to overall survival rate. Furthermore, the machine learning calcification models show good performance on the determined biomarkers. Moreover, the literature reports have confirmed all of the identified gene biomarkers for breast cancer. According to the literature evidence, the identified hub genes are highly correlated with HER2-negative breast cancer. The 53-mRNA signature might be a potential gene set for TNM based stages as well as possible therapeutics with potentially good performance in predicting and managing recurrence-free survival rates at stages I, II, III, and IV as well as in the integrated group. Moreover, the identified genes for the TNM-based stages can also be used as mRNA profile signatures to determine the current stage of the breast cancer.

Knockdown of Orphan Transporter SLC22A18 Impairs Lipid Metabolism and Increases Invasiveness of HepG2 Cells

PURPOSE

The aim of this work is to investigate the roles of solute carrier family 22 member 18 (SLC22A18) in lipid metabolism and in establishing the tumor phenotype of HepG2 cells.

METHODS

SLC22A18-knockdown HepG2 cells were established by stable transfection with shRNA. Protein expression levels were measured by quantitative proteomics and Western blot analysis. Cell growth was examined by cell counting kit. Accumulation of triglyceride-rich lipid droplets was measured by Oil-Red O staining. Cell migration and invasion were examined by Transwell assays.

RESULTS

SLC22A18-knockdown HepG2 cells accumulated triglyceride-rich lipid droplets and showed decreased expression levels of lysosomal/autophagic proteins, suggesting that lipid degradation is suppressed. Growth of HepG2 cells was decreased by SLC22A18 knockdown, but was restored by free fatty acid supplementation. In addition, SLC22A18 knockdown decreased the expression of insulin-like growth factor-binding protein 1 (IGFBP-1) and increased the invasion ability of HepG2 cells. Exogenous IGFBP-1 blocked the increase of invasion activity induced by SLC22A18 knockdown.

CONCLUSION

Our results suggest that suppression of SLC22A18 decreased the supply of intracellular free fatty acids from triglyceride-rich lipid droplets by impairing the lysosomal/autophagy degradation pathway and reduced the invasive activity of HepG2 cells by decreasing IGFBP-1 expression.

SLC transporters as a novel class of tumour suppressors: identity, function and molecular mechanisms

The role of plasma membrane transporters in cancer is receiving increasing attention in recent years. Several transporters for essential nutrients are up-regulated in cancer and serve as tumour promoters. Transporters could also function as tumour suppressors. To date, four transporters belonging to the SLC gene family have been identified as tumour suppressors. SLC5A8 is a Na(+)-coupled transporter for monocarboxylates. Among its substrates are the bacterial fermentation products butyrate and propionate and the ubiquitous metabolite pyruvate. The tumour-suppressive function of this transporter relates to the ability of butyrate, propionate and pyruvate to inhibit histone deacetylases (HDAC). SLC5A8 functions as a tumour suppressor in most tissues studied thus far, and provides a molecular link to Warburg effect, a characteristic feature in most cancers. It also links colonic bacteria and dietary fibre to the host. SLC26A3 as a tumour suppressor is restricted to colon; it is a Cl(-)/HCO(-) 3 exchanger, facilitating the efflux of HCO(-) 3 The likely mechanism for the tumour-suppressive function of SLC26A3 is related to intracellular pH regulation. SLC39A1 is a Zn(2+) transporter and its role in tumour suppression has been shown in prostate. Zn(2+) is present at high concentrations in normal prostate where it elicits its tumour-suppressive function. SLC22A18 is possibly an organic cation transporter, but the identity of its physiological substrates is unknown. As such, there is no information on molecular pathways responsible for the tumour-suppressive function of this transporter. It is likely that additional SLC transporters will be discovered as tumour suppressors in the future.

Characterization of SLC22A18 as a tumor suppressor and novel biomarker in colorectal cancer

SLC22A18, solute carrier family 22, member 18, has been proposed to function as a tumor suppressor based on its chromosomal location at 11p15.5, mutations and aberrant splicing in several types of cancer and down-regulation in glioblastoma. In this study, we sought to demonstrate the significance of SLC22A18 as a tumor suppressor in colorectal cancer (CRC) and provide mechanistic bases for its function. We first showed that the expression of SLC22A18 is significantly down-regulated in tumor tissues using matched normal-tumor samples from CRC patients. This finding was also supported by publically accessible data from The Cancer Genome Atlas (TCGA). Functionally, SLC22A18 inhibits colony formation and induces of G2/M arrest consistent with being a tumor suppressor. Interestingly, suppression of KRAS by RNA interference promotes SLC22A18 expression, and expression of SLC22A18 in turn inhibits KRAS^G12D-mediated anchorage independent growth of NIH3T3 cells indicating a mutual negative interaction. Finally, we evaluated diagnostic and prognostic values of SLC22A18 using clinical and gene expression data from TCGA which revealed a significantly worse long-term prognosis for patients with low level SLC22A18 expression. In sum, we established SLC22A18 as a tumor suppressor in colon epithelial cells and propose that SLC22A18 is potentially a marker of diagnostic and prognostic values.

microRNA-137 functions as a tumor suppressor in human non-small cell lung cancer by targeting SLC22A18

Our previous study demonstrated that the overexpression of solute carrier family 22 member 18 (SLC22A18) in human non-small cell lung cancer (NSCLC) tissues might be associated with tumor progression and patients' prognosis. The aim of this study was to investigate the molecular mechanisms underlying its roles in NSCLC. As a result, bioinformatics analysis and luciferase reporter assay showed that microRNA (miRNA)-137 directly targeted SLC22A18 in NSCLC cells. Then, functional studies indicated that the ectopic expression of miR-137 significantly inhibited NSCLC cell proliferation, invasion and migration by targeting SLC22A18. More importantly, the decreased expression of miR-137 in clinical NSCLC tissues was correlated with advanced TNM stage, positive metastasis and poor prognosis of patients with this malignancy. In conclusion, these findings offer the convincing evidence that the roles of SLC22A18 in NSCLC progression may be partially caused by the regulatory effects of miR-137, which may function as a tumor suppressor. Our clinical data further indicated that miR-137 may be an independent favorable prognostic factor in NSCLC patients.

The association between the expression of solute carrier transporters and the prognosis of pancreatic cancer

OBJECTIVES

The aim of this study was to investigate the prognostic significance of fourteen anticancer drug-relevant solute carrier transporters (SLCs) in pancreatic cancer in the context of clinical-pathological characteristics and the KRAS mutation status of tumors.

METHODS

Tumors and non-neoplastic pancreatic tissues were obtained from 32 histologically verified patients with pancreatic ductal adenocarcinoma. The transcript profile of SLCs was assessed using quantitative real-time PCR. KRAS mutations in exon 2 were assessed by high-resolution melting analysis and confirmed by sequencing.

RESULTS

SLC22A3 and SLC22A18 were upregulated and SLC22A1, SLC22A2, SLC22A11, SLC28A1, SLC28A3 and SLC29A1 were downregulated when compared with non-neoplastic pancreatic tissues. Moreover, significantly lower levels of SLC22A1, SLC22A11 and SLC29A1 were found in tumors with angioinvasion. There was also a significantly higher transcript level of SLC28A1 in tumors with regional lymph nodes affected by metastasis. The study found that a high expression of SLC28A1 was significantly associated with poor overall survival in unselected patients. In contrast, a high expression of SLC22A3 or SLC29A3 was significantly associated with longer overall survival in patients treated with nucleoside analogs. Protein expression of SLC22A1, SLC22A3 and SLC29A3 in tumor tissues of patients with pancreatic carcinoma was observed by immunoblotting for the first time. Finally, SLC levels were not found to be associated with KRAS mutation status in exon 2.

CONCLUSIONS

This study identified a number of associations of transcript levels of SLCs with prognosis of pancreatic cancer patients.

Dysregulated methylation at imprinted genes in prostate tumor tissue detected by methylation microarray

Background

Imprinting is an important epigenetic regulator of gene expression that is often disrupted in cancer. While loss of imprinting (LOI) has been reported for two genes in prostate cancer (IGF2 and TFPI2), disease-related changes in methylation across all imprinted gene regions has not been investigated.

Methods

Using an Illumina Infinium Methylation Assay, we analyzed methylation of 396 CpG sites in the promoter regions of 56 genes in a pooled sample of 12 pairs of prostate tumor and adjacent normal tissue. Selected LOI identified from the array was validated using the Sequenom EpiTYPER assay for individual samples and further confirmed by expression data from publicly available datasets.

Results

Methylation significantly increased in 52 sites and significantly decreased in 17 sites across 28 unique genes (P < 0.05), and the strongest evidence for loss of imprinting was demonstrated in tumor suppressor genes DLK1, PLAGL1, SLC22A18, TP73, and WT1. Differential expression of these five genes in prostate tumor versus normal tissue using array data from a publicly available database were consistent with the observed LOI patterns, and WT1 hypermethylation was confirmed using quantitative DNA methylation analysis.

Conclusions

Together, these findings suggest a more widespread dysregulation of genetic imprinting in prostate cancer than previously reported and warrant further investigation.