Transcriptomic signature predicts the distant relapse in patients with ER+ breast cancer treated with tamoxifen for five years

FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma

Simple Summary

Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM.

Abstract

Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.

Functional and pathologic association of aminoacyl-tRNA synthetases with cancer

Although key tumorigenic and tumor-suppressive factors have been unveiled over the last several decades, cancer remains the most life-threatening disease. Multiomic analyses of patient samples and an in-depth understanding of tumorigenic processes have rapidly revealed unexpected pathologic associations of new cellular factors previously overlooked in cancer biology. In this regard, the newly discovered activities of human aminoacyl-tRNA synthases (ARSs) deserve attention not only for their pathological significance in tumorigenesis but also regarding diagnostic and therapeutic implications. ARSs are not only essential enzymes covalently linking substrate amino acids to cognate tRNAs for protein synthesis but also function as regulators of cellular processes by sensing different cellular conditions. With their catalytic role in protein synthesis and their regulatory role in homeostasis, functional alterations or dysregulation of ARSs might be pathologically associated with tumorigenesis. This review focuses on the potential implications of ARS genes and proteins in different aspects of cancer based on various bioinformatic analyses and experimental data. We also review their diverse activities involving extracellular secretion, protein–protein interactions, and amino acid sensing, which are related to cancers. The newly discovered cancer-related activities of ARSs are expected to provide new opportunities for detecting, preventing and curing cancers.

Enzymes called aminoacyl-tRNA synthetases (ARSs), which play a central role in all life, are becoming implicated in several aspects of cancer in ways that may lead to new approaches for prevention, detection and treatment. ARS enzymes catalyse the ligation of amino acids to transfer RNA molecules to allow amino acids to combine in the correct sequences to form proteins. Jung Min Han, Sunghoon Kim and colleagues at Yonsei University, Incheon, South Korea, review researches implicating ARS enzymes and the genes that code for them in a variety of cancers. The behavior of ARS enzymes and their genes are found to be altered in several types of cancer cells in ways that may either initiate or support the onset and development of the disease, through which they could be suggested as targets for novel anti-cancer drugs.

Identification and Integrate Analysis of Key Biomarkers for Diagnosis and Prognosis of Non-Small Cell Lung Cancer Based on Bioinformatics Analysis

Background: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer affecting humans. However, appropriate biomarkers for diagnosis and prognosis have not yet been established. Here, we evaluated the gene expression profiles of patients with NSCLC to identify novel biomarkers. Methods: Three datasets were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes were analyzed. Venn diagram software was applied to screen differentially expressed genes, and gene ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Cytoscape was used to analyze protein-protein interactions (PPI) and Kaplan–Meier Plotter was used to evaluate the survival rates. Oncomine database, Gene Expression Profiling Interactive Analysis (GEPIA), and The Human Protein Atlas (THPA) were used to analyze protein expression. Quantitative real-time polymerase (qPCR) chain reaction was used to verify gene expression. Results: We identified 595 differentially expressed genes shared by the three datasets. The PPI network of these differentially expressed genes had 202 nodes and 743 edges. Survival analysis identified 10 hub genes with the highest connectivity, 9 of which (CDC20, CCNB2, BUB1, CCNB1, CCNA2, KIF11, TOP2A, NDC80, and ASPM) were related to poor overall survival in patients with NSCLC. In cell experiments, CCNB1, CCNB2, CCNA2, and TOP2A expression levels were upregulated, and among different types of NSCLC, these four genes showed highest expression in large cell lung cancer. The highest prognostic value was detected for patients who had successfully undergone surgery and for those who had not received chemotherapy. Notably, CCNB1 and CCNA2 showed good prognostic value for patients who had not received radiotherapy. Conclusion: CCNB1, CCNB2, CCNA2, and TOP2A expression levels were upregulated in patients with NSCLC. These genes may be meaningful diagnostic biomarkers and could facilitate the development of targeted therapies.

Identification of CCNB2 as A Potential Non-Invasive Breast Cancer Biomarker in Peripheral Blood Mononuclear Cells Using The Systems Biology Approach

OBJECTIVE

Breast cancer (BC) still remains an imperative clinical issue, despite advances in the diagnosis, prognosis and treatment modalities of this malignancy. Hence, progress has been made to identify non-invasive, high sensitive and specific biomarkers. Since immune system affects development of breast cancer, peripheral blood mononuclear cells (PBMCs) -a subpopulation of immune cells- can be considered as a promising tool in the field of BC biomarker research. In the current study, we initially attempted to use concept of the present shared biomarkers in solid tumors and systemic immune profile and then evaluate correlation of these biomarkers to clinical use in cancer research.

MATERIALS AND METHODS

In this experimental study, available microarray gene expression datasets of BC as well as the related PBMCs were retrieved and downloaded from the Gene Expression Omnibus (GEO) database, followed by analysis using GEO2R along with affylmGUI, a R-based package, to obtain differentially expressed genes (DEGs). Signature genes from 20 types of cancer were also applied to validate DEGs. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was carried out to assess mRNA level of CCNB2 in PBMC of the BC patients and healthy subjects.

RESULTS

DEGs analysis for the transcription profile of BC cells and PBMCs showed two shared targets, CCNB2 and PGK1. Validation with systems biology using reweighted 20 types of cancer signature genes revealed that CCNB2 is the only common target in BC and its related PBMCs, which was further validated by qRT-PCR implying a significant increase in the level of CCNB2 in the BC patients.

CONCLUSION

Results of this study demonstrated that PBMCs are affected by BC cells and CCNB2 may be of value as a diagnostic biomarker for breast cancer. However, verification would require future detailed experimental plans.

Identification of Ten Mitosis Genes Associated with Tamoxifen Resistance in Breast Cancer

Background

Endocrine therapy is the backbone therapy in estrogen receptor α (ER)-positive breast cancer, and tamoxifen resistance is a great challenge for endocrine therapy. Tamoxifen-resistant and sensitive samples from the international public repository, the Gene Expression Omnibus (GEO) database, were used to identify therapeutic biomarkers associated with tamoxifen resistance.

Materials and Methods

In this study, integrated analysis was used to identify tamoxifen resistance-associated genes. Differentially expressed genes (DEGs) were identified. Gene ontology and pathway analysis were then analyzed. Weighted correlation network analysis (WGCNA) was performed to find modules correlated with tamoxifen resistance. Protein–protein interaction (PPI) network was used to find hub genes. Genes of prognostic significance were further validated in another GEO dataset and cohort from Shanghai Ruijin Hospital using RT-PCR.

Results

A total of 441 genes were down-regulated and 123 genes were up-regulated in tamoxifen-resistant samples. Those up-regulated genes were mostly enriched in the cell cycle pathway. Then, WGCNA was performed, and the brown module was correlated with tamoxifen resistance. An overlap of 81 genes was identified between differentially expressed genes (DEGs) and genes in the brown module. These genes were also enriched in the cell cycle. Twelve hub genes were identified using PPI network, which were involved in the mitosis phase of the cell cycle. Finally, 10 of these 12 genes were validated to be up-regulated in tamoxifen-resistant patients and were associated with poor prognosis in ER-positive patients.

Conclusion

Our study suggested mitosis-related genes are mainly involved in tamoxifen resistance, and high expression of these genes could predict poor prognosis of patients receiving tamoxifen. These genes may be potential targets to improve efficacy of endocrine therapy in breast cancer, and inhibitors targeted these genes could be used in endocrine-resistant patients.

WSB2 as a target of Hedgehog signaling promoted the malignant biological behavior of Xuanwei lung cancer through regulating Wnt/β-catenin signaling

Background

Lung cancer represents the most leading causes of cancer-related deaths worldwide, especially in Xuanwei in eastern Yunnan province, China. WD repeat and SOCS box containing protein (WSB) has been reported to participate in the carcinogenesis of lung cancer. However, there is no report about the role of WSB2 in the carcinogenesis and development of lung cancer in Xuanwei. Here, we investigated the functional role of WSB2 in Xuanwei lung cancer and uncovered its underlying molecular mechanisms.

Methods

The expression of WSB2 in lung cancer cell lines and tissues were measured using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Western blotting was used to determine the protein levels of WSB2, E-cadherin, N-cadherin, vimentin, c-Myc and β-catenin in lung cancer cells. Cell viability was detected using 3-(4,5-diethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-etrazolium, inner salt (MTS) assay. While cell apoptosis and cell cycle distribution were quantified using flow cytometry following indicated staining. The change of cell invasion ability was detected using Transwell assay. FH535 was employed to block Wnt/β-catenin pathway. A xenograft tumor model was applied to confirm the tumor properties of WSB2 in vivo.

Results

Our data showed that WSB2 was frequently up-regulated in Xuanwei lung cancer tissues and cells, when compared with paired non-cancerous tissues and normal lung epithelial cells. Knockdown of WSB2 notably reduced cell viability, cell invasion, epithelial-mesenchymal transition (EMT) process, while induced apoptotic cell death and cell cycle arrest of Xuanwei lung cancer cells. Moreover, in vivo findings also confirmed that WSB2 knockdown could effectively delay the growth of tumor. Mechanistic studies revealed that c-Myc and β-catenin were notably decreased at both protein and mRNA levels after knocking down of WSB2, while overexpression of WSB2 showed a contrary tendency. In addition, blocking Wnt/β-catenin pathway using FH535 rescued the cancer promoting effect mediated by overexpression of WSB2. Furthermore, WSB2 activated Wnt/β-catenin pathway and accelerated the progression of lung cancer.

Conclusions

WSB2 promoted the progression of lung cancer in Xuanwei by triggering Wnt/β-catenin signaling pathway.

Study of Gene Expression Profiles of Breast Cancers in Indian Women

Breast cancer is the most common cancer among women globally. In India, the incidence of breast cancer has increased significantly during the last two decades with a higher proportion of the disease at a young age compared to the west. To understand the molecular processes underlying breast cancer in Indian women, we analysed gene expression profiles of 29 tumours and 9 controls using microarray. In the present study, we obtained 2413 differentially expressed genes, consisting of overexpressed genes such as COL10A1, COL11A1, MMP1, MMP13, MMP11, GJB2, and CST1 and underexpressed genes such as PLIN1, FABP4, LIPE, AQP7, LEP, ADH1A, ADH1B, and CIDEC. The deregulated pathways include cell cycle, focal adhesion and metastasis, DNA replication, PPAR signaling, and lipid metabolism. Using PAM50 classifier, we demonstrated the existence of molecular subtypes in Indian women. In addition, qPCR validation of expression of metalloproteinase genes, MMP1, MMP3, MMP11, MMP13, MMP14, ADAMTS1, and ADAMTS5 showed concordance with that of the microarray data; wherein we found a significant association of ADAMTS5 down-regulation with older age (≥55 years) of patients. Together, this study reports gene expression profiles of breast tumours from the Indian subcontinent, throwing light on the pathways and genes associated with the breast tumourigenesis in Indian women.

The multisystemic functions of FOXD1 in development and disease

Transcription factors (TFs) participate in a wide range of cellular processes due to their inherent function as essential regulatory proteins. Their dysfunction has been linked to numerous human diseases. The forkhead box (FOX) family of TFs belongs to the "winged helix" superfamily, consisting of proteins sharing a related winged helix-turn-helix DNA-binding motif. FOX genes have been extensively present during vertebrates and invertebrates' evolution, participating in numerous molecular cascades and biological functions, such as embryonic development and organogenesis, cell cycle regulation, metabolism control, stem cell niche maintenance, signal transduction, and many others. FOXD1, a forkhead TF, has been related to different key biological processes such as kidney and retina development and embryo implantation. FOXD1 dysfunction has been linked to different pathologies, thereby constituting a diagnostic biomarker and a promising target for future therapies. This paper aims to present, for the first time, a comprehensive review of FOXD1's role in mouse development and human disease. Molecular, structural, and functional aspects of FOXD1 are presented in light of physiological and pathogenic conditions, including its role in human disease aetiology, such as cancer and recurrent pregnancy loss. Taken together, the information given here should enable a better understanding of FOXD1 function for basic science researchers and clinicians.