Analysis of Changes in the Expression of Selected Genes from the ABC Family in Patients with Triple-Negative Breast Cancer

The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer

Background

Triple-negative breast cancer (TNBC) is a heterogeneous disease with a worse prognosis. Despite ongoing efforts, existing therapeutic approaches show limited success in improving early recurrence and survival outcomes for TNBC patients. Therefore, there is an urgent need to discover novel and targeted therapeutic strategies, particularly those focusing on the immune infiltrate in TNBC, to enhance diagnosis and prognosis for affected individuals.

Methods

The gene co-expression network and gene ontology analyses were used to identify the differential modules and their functions based on the GEO dataset of GSE76275. The Weighted Gene Co-Expression Network Analysis (WGCNA) was used to describe the correlation patterns among genes across multiple samples. Subsequently, we identified key genes in TNBC by assessing genes with an absolute correlation coefficient greater than 0.80 within the eigengene of the enriched module that were significantly associated with breast cancer subtypes. The diagnostic potential of these key genes was evaluated using receiver operating characteristic (ROC) curve analysis with three-fold cross-validation. Furthermore, to gain insights into the prognostic implications of these key genes, we performed relapse-free survival (RFS) analysis using the Kaplan-Meier plotter online tool. CIBERSORT analysis was used to characterize the composition of immune cells within complex tissues based on gene expression data, typically derived from bulk RNA sequencing or microarray datasets. Therefore, we explored the immune microenvironment differences between TNBC and non-TNBC by leveraging the CIBERSORT algorithm. This enabled us to estimate the immune cell compositions in the breast cancer tissue of the two subtypes. Lastly, we identified key transcription factors involved in macrophage infiltration and polarization in breast cancer using transcription factor enrichment analysis integrated with orthogonal omics.

Results

The gene co-expression network and gene ontology analyses revealed 19 modules identified using the dataset GSE76275. Of these, modules 5, 11, and 12 showed significant differences between in breast cancer tissue between TNBC and non-TNBC. Notably, module 11 showed significant enrichment in the WNT signaling pathway, while module 12 demonstrated enrichment in lipid/fatty acid metabolism pathways. Subsequently, we identified SHC4/KCNK5 and ABCC11/ABCA12 as key genes in module 11 and module 12, respectively. These key genes proved to be crucial in accurately distinguishing between TNBC and non-TNBC, as evidenced by the promising average AUC value of 0.963 obtained from the logistic regression model based on their combinations. Furthermore, we found compelling evidence indicating the prognostic significance of three key genes, KCNK5, ABCC11, and ABCA12, in TNBC. Finally, we also identified the immune cell compositions in breast cancer tissue between TNBC and non-TNBC. Our findings revealed a notable increase in M0 and M1 macrophages in TNBC compared to non-TNBC, while M2 macrophages exhibited a significant reduction in TNBC. Particularly intriguing discovery emerged with respect to the transcription factor FOXM1, which demonstrated a significant regulatory role in genes positively correlated with the proportions of M0 and M1 macrophages, while displaying a negative correlation with the proportion of M2 macrophages in breast cancer tissue.

Conclusion

Our research provides new insight into the biomarkers and immune infiltration of TNBC, which could be useful for clinical diagnosis of TNBC.

Patterns of breast cancer locoregional relapse, metastasis, and subtypes in Ghana

BACKGROUND

Significant advances have been made in targeted therapeutics and systemic therapy regimens for breast cancer (BC) treatment over the past decade. Tumour cells can however remain in the body, leading to locoregional relapse and/or metastasis. Subtypes of BC have distinct prognostic effects and have been linked to varying risks of early locoregional relapse and metastases, response to treatment, and overall survival. Most Low- and middle-income countries (LMICs) have no registries of BC locoregional relapse and metastasis.

METHODS

This study comprehensively reviewed, a 3-year retrospective single-centre data of female BC visiting the Komfo Anokye Teaching Hospital (KATH), Ghana to determine the prevalence of locoregional relapse and metastasis across our patient population. Prevalence of metastasis among the various BC subtypes was also determined.

RESULTS

Prevalence of BC locoregional relapse and metastasis were 3.4% and 47.6% respectively. For BC patients with documented locoregional relapse (N = 36), 27.8% (CI = 15.8 - 44.0%) had relapse to the contralateral breast, 41.7% (CI = 27.1 - 57.8%) had relapse to the ipsilateral breast, and 30.6% (CI = 18.0 - 46.9%) had relapse to regional lymph nodes. For BC patients with documented metastasis (N = 503), 151 (30%) had multiple organs involvement, 141 (28%) had lung metastases, 80 (16%) had bone metastases, 45 (9%) had liver metastases, 16 (3%) had brain metastases and 70 (14%) had other metastases (ovary, uterus, spleen, peritoneum, or distant lymph nodes). Basal subtype was the most common subtype (n = 82, 41%), followed by Luminal A (n = 69, 34.5%), HER2+ (n = 37, 18.5%) and Luminal B (n = 12, 6%). Basal subtypes had the most metastasis (35%), with multiple metastasis being the most prevalent (13%).

CONCLUSION

Close to half of the patients (46%) presented with metastatic BC. BC subtypes could influence the specific metastatic site. The most common BC subtype was the Basal subtype and had the most metastases (35%), with multiple metastasis being the most prevalent (13%). These findings should serve as a guide in the management of patients to enhance early prediction and detection of locoregional relapse and metastasis for improved overall treatment outcomes.

Transcriptome mining and expression analysis of ABC transporter genes in a monophagous herbivore, Leucinodes orbonalis (Crambidae: Lepidoptera)

Insecticide resistance is a global concern and requires immediate attention to manage dreadful insect pests. One of the resistance mechanisms adopted by insects is through ATP-binding cassette (ABC) transporter proteins. These proteins rapidly transport and eliminate the insecticidal molecules across the lipid membranes (Phase III detoxification mechanism). In the present study, we investigated the potential role of ABC transporter genes in imparting insecticide resistance in field-collected insecticide resistant larvae of eggplant shoot and fruit borer (Leucinodes orbonalis; Crambidae: Lepidoptera). Dose-mortality bioassays against five insecticidal molecules revealed moderate to high levels of insecticide resistance (32.2. to 134.1-fold). Thirty-one genes encoding ABC transporter proteins were mined from the transcriptome resources of L. orbonalis. They were classified under eight sub-families (ABCA to ABCH). Phylogenetic analysis indicated ABCG is the most divergent, composed of nine genes as compared to many other insects. Transcriptome analysis of the insecticide resistant and susceptible strains of L. orbonalis revealed differential expression of 13 ABC transporter genes. The altered expression of these genes was further validated using qRT-PCR. The knockdown studies indicated the involvement of ABCD1 and ABCG2 genes in chlorantraniliprole resistance in the insecticide-resistant strain of L. orbonalis. This study unveils the additional mechanisms employed by L. orbonalis in resisting insecticide toxicity through accelerated excretion mode. These ABCD and ABCG family genes could be candidate targets in developing genome-assisted pest management strategies in the future.

Overexpression of ABCB1 confers resistance to FLT3 inhibitor FN-1501 in cancer cells: in vitro and in vivo characterization

FN-1501 is a potent FLT3 inhibitor with antitumor activity. A phase 1 trial of FN-1501 monotherapy in patients with advanced solid tumors and R/R AML is in progress. Since one of the primary causes of multidrug resistance (MDR) is the overexpression of ATP-binding cassette superfamily B member 1 (ABCB1), the objective of this study was to investigate the potential relationship between FN-1501 and the ABCB1 transporter. We found ABCB1 overexpressing-cancer cells conferred FN-1501 resistance, which could be reversed by an ABCB1 inhibitor. Molecular docking study revealed that FN-1501 docked the ligand binding site with an affinity score of -9.77 kcal/mol, denoting a strong interaction between FN-1501 and ABCB1. Additionally, the ABCB1 ATPase assay indicated that FN-1501 could significantly stimulate ABCB1 ATPase activity. Furthermore, we observed a similar trend of ABCB1-facilated FN-1501 resistance in tumor-bearing mice model. In sum, we demonstrate that FN-1501 is a substrate of ABCB1 transporter from both in vivo and in vitro studies. Therefore, our findings provide new insight on the mechanism of chemoresistance due to ABCB1 overexpression.

Increased Expression of the ABCA1 and ABCA3 Transporter Genes is Associated with Cisplatin Resistance in Breast Cancer Cells

OBJECTIVE

Breast cancer (BC) is a highly malignant neoplasm with resistance to therapeutics that are related to genes associated with multidrug resistance. The excessive expression of ATP-binding cassette transporters (ABCs) genes, including ABCA1 and ABCA3, is a primary factor contributing to the increased effluent of cell-toxic drugs and subsequent treatment resistance. Therefore, the current work aimed to explore the role of ABCA1 and ABCA3 in chemoresistance activity against cisplatin in breast cancer cells.

METHODS

The current study compared the AMJ13 breast cancer cells derived from a woman Iraqi patient, which are hormone receptor-negative, with MCF-7 breast cancer cells, which are hormone receptor-positive.  Cytotoxic assay (CCK-8 assay) is used to measure the cell's viability and cytotoxic activity after it has been treated with cisplatin. Morphological Study using crystal violet stain to examine cytological changes was conducted. Quantitative RT-PCR is used to measure how much the ABCA1, and 3 genes mRNA are being expressed before and after treatment.

RESULTS

The CCK-8 assay found that IC50 values of cisplatin in AMJ13 and MCF-7 cells were 202.2 µg/ml and 90.23 µg/ml, respectively. The IC50 value of AMJ13 is 2-fold higher than in MCF-7 cells. The QPCR study revealed that breast cancer cell lines AMJ13 and MCF-7 subjected to cisplatin showed upregulated levels of ABCA1 and ABCA3 expression. Experiments with cytotoxicity assays demonstrate that higher expression of ABCA1 and ABCA3 in AMJ13 and MCF-7 breast cancer cell lines is linked to their resistance.  Conclusion: The findings of this study suggest that the ABCA1 and ABCA3 transporters play a significant role in the resistance to cisplatin and,.